Troubleshooting microgreens can seem overwhelming, but there are usually a few root causes to most of the problems that develop.

The best way to get better at growing and troubleshooting microgreens is of course to keep growing and experimenting with new varieties, methods, and equipment, but also to do a lot of reading!

How to use this troubleshooting guide:

Each of the sections will have a specific microgreen problem as the heading. Then the paragraph will walk you through the most common causes, and link to more information so you can dig in deeper.

To find your problem quickly try using search: Hold CTRL + F on a PC, or Command + F on a mac and type in your problem in a few words. For example if your microgreens are getting moldy, try searching for “mold”.

You can also check the table of contents below (sorry it’s so long!):

Microgreens are too hard to grow, what can I do?

It can seem daunting at first, but if you break it down into steps, and master each one as you go, it gets a lot easier. If there are a specific issue you’re having, and you can figure out what it is, you’ll be growing microgreens like it’s no big deal in no time.

There are some harder to grow varieties. Try starting out with simpler microgreens like pea shoot, broccoli, or radish. There’s a ton of information online, and as long as you use the right supplies and equipment, you shouldn’t have a problem.

Stick with it, I’m here to help and you’re probably just a little bit of reading away from unlocking the knowledge that you need to succeed.

Seeds won’t germinate

Seeds are the core of your microgreen success. Everything starts and ends with the seeds. If you start with bad seeds, there’s nothing you can do to, so get the highest quality seeds you can.

If your seeds won’t germinate, you want to systematically walk through the potential causes, and make sure it’s not something in your process or the techniques you’re using that are causing a problem.

Non-seed causes of poor germination:

  • Too old: seeds that’s aren’t stored under ideal conditions  (consistently frozen, and dark) can degrade over time. If they’re exposed to any moisture, temperature fluctuations, or any temperatures above freezing they can start to decompose, and drop in viability and vigor.
  • Bad source: you might be doing everything right on your end, but if your seed supplier isn’t using pest and bird proof containers, and selling you fresh, well-tested seed (high germination rates, low pathogens), you could be fighting an uphill battle. I recommend my favorite seed suppliers here.

Seed quality issues:

  • Your seeds might be TOO FRESH! I didn’t believe it at first, but it’s possible for extremely fresh seeds to still be a dormant period. Some seeds have evolved to go dormant during unfavorable seasons, so they don’t germinate going into a dry season, or going into winter.
  • Unspecialized seeds: While you can grow microgreens with any seeds, microgreen seed varieties have often been carefully chosen to germinate all at the same time, and quickly. When you’re growing vegetables, a few days or a week difference doesn’t matter, but for microgreens this could cut your yields in half.
  • Poor storage: If seeds get too hot, too moist, or cycle between hot and cold too many times, their quality can degrade. Viability and vigor can both suffer. If seeds are exposed to humidity and then dry out, they may partially germinate then die, or they may begin to grow mold or other pathogens. Microgreen seed storage is very important.

To make sure you’re not using unsafe seeds or your supplier didn’t give you something unsuitable for microgreens, read more here:

How to Store Microgreen Seeds for Long Shelf-life & Vigorous Germination

Uneven or slow germination

Even germination is accomplished by having the following dialed in: fresh high quality seeds, long enough soaking (especially for sunflower and peas), good seed to soil contact (through a weighted blackout period), and enough moisture in the soil.

If you’re not using a blackout period, with another tray pressing your microgreens into moist soil, they might not be getting enough moisture to fully germinate.

Unfortunately you might be stuck with low-quality seeds. You can do a quick test in moist paper towel in a ziplock bag. Make sure there’s some air in the bag so they’re not fully underwater (seeds can drown). And ask your seed supplier about the lot that you bought, they should have germination rates.

Slow germination

Most seeds germinate in 2-3 days. At the end of a 24 hour soak some vigorous seeds will already be germinating. Some are slower, but if things are really taking forever, you might have low quality seeds, but the most likely cause is too little moisture.

Seeds need a good soak for the first day or two to get germinating. For small seeds you can put them directly on to moist soil (and cover to keep the humidity and moisture in), but for larger seeds like sunflower or peas, you’ll want to soak them for up to 24 hours.

Mucilaginous seeds won’t germinate and grow well

Some seeds form a gelly/goopy substance called mucilage. All seeds form a little bit, but quinoa, basil, brown mustard, and chia make a lot of this stuff.

When you hydrate the tiny seeds, they absorb water and make a layer of sticky stuff. It’s mostly made up of pectin (fruit jam thickener) and hemicellulose, and it sure makes microgreens trickier to grow.

Allelopathy is something basil in particular does. It secretes a natural herbicide that prevents nearby seeds from growing.

To get the best mucilaginous seed crops you’ll want to dig into some specific tips and techniques in these two articles:

What are Mucilaginous Microgreens? Brilliant Tips for Successful Grows

Hardest Microgreens to Grow & Secrets to Success

Re-used microgreen soil smells bad

All soil should smell rich and earthy. There shouldn’t be any smell of decomposition, like rotten food, or sour smells.

Definitely don’t re-use microgreen soil directly for indoor microgreens! Especially not without composting. The left-over seeds, roots, and stems will grow mold and you’ll get terrible results. More on that here.

My paper towel microgreens won’t work

I don’t recommend growing microgreens on paper towel if you can avoid it. I haven’t had much success or experience growing on paper towels, so my top recommendation would be to give them a little bit of soil. Soil will do a better job retaining moisture, and gives them some nutrients, they don’t need much.

Hydroponic Growing Mats/Pads Smell Bad, Like Rubber

If you’re growing hydroponically, especially with coconut fiber mats, the smell of rubber is something you might just need to get used to.

The latex that’s used to bind grow mats together has the rubbery smell. Latex comes from natural sources, it’s in a white milky fluid that’s secreted by a lot of plants, but it can also have additives like casein (a rubber softener separated from milk), which isn’t strictly vegan. It might smell funny, but it’s the growing media, and not your microgreens so the smell shouldn’t linger in your final product.

Too much leftover soil from spent trays, what can I do with it?

Once you’ve been growing microgreens for a while, you probably have a pile of soil, roots, and cut-off stems. This stuff makes incredible compost. The tender roots and stems decompose quickly and make a rich, nutrient dense soil.

Definitely don’t re-use microgreen soil without composting, the left-over seeds, roots, and stems will grow mold and you’ll get terrible results. More on that here.

It’s not worth trying to use your own compost for growing microgreens indoors. The insects and micro-biome from your garden will thrive and cause all kinds of problems in your house. But home-made compost is incredible for the garden or growing outside.

If you want to get your compost pile in tip top shape, read this:

Should I cover compost? Composting for beginners

Potting Soil has clumps and branches

An even, fine soil texture helps microgreens germinate and grow more evenly. Because we’re not using that much soil, I recommend 1” or less, it’s worth taking a few extra minutes to set things up for success. Clumpy soil that has debris like branches can be strained.

You can buy soil sieves online for really cheap, but I’d advice getting one that’s at least 12 inches across, it makes it a lot easier to keep the soil where you want it (avoid making a mess). This one is pretty similar to the one I use, mine’s square but this one’s even better, it fits nicely on a 5 Gallon pale. A ¼” or 3/8” mesh size works great for fine soils.

SE Patented Stackable 13-1/4″ Sifting Pan, 1/4″ Mesh Screen – GP2-14 (Links to Amazon)

Another option is to buy finer soil. Some soils will be screened more carefully, and have finer grains, but they’re usually a little more expensive. Ask your local garden center what they would recommend or check out my recommended soils here.

Soil on the greens at harvest

Dirt can carry pathogens like mold and bacteria. We want to avoid getting it on the harvested microgreens if possible. There are three main causes of soil on microgreens:

  • Burying the seeds
  • Harvesting Technique
  • Seed hulls carrying dirt up into the foliage

One of the main ways people get soil on their microgreens is by burying the seeds. In nature or out in the garden most seeds grow best if they’re under at least some soil, but it’s a little different for microgreens. Because we’re growing inside, we have a few tricks to mimic the moist, dark conditions that seeds want for germination.

All the microgreens I’ve run into can be grown by putting the seeds right on top of the soil. Pat the soil down lightly first, then spread the seeds evenly on the top of the soil. When you add water, add it from the bottom (between trays) and the seeds won’t be disturbed.

Then by placing a second tray directly on top and pressing the seeds into the soil moisture is trapped and it creates a perfect dark germination chamber. It also ensures really good seed-to-soil contact, but the greens don’t have to push through soil as they grow, so the stems and cotyledons are less likely to pick up soil. Brush up on the key microgreen steps here.

If you’re not careful when you’re harvesting, you can pick up soil and get it on your final product. I put goether a great guide on harvesting microgreens that you should check out.

Another cause of soil on microgreens is from soil sticking to the seed hulls. The seed hulls that never fall off the microgreens can carry soil up into the foliage. Follow these tricks to help seed hulls shed, sunflower microgreens have massive problems with shedding seed hulls, big hulls that need just the right conditions to fall off.

Can’t find hydrogen peroxide locally

Sometimes it can be hard to find hydrogen peroxide (H2O2) locally. Hydrogen peroxide has a lot of different uses, and comes packaged mainly for food-safe, first-aid, and industrial uses.

Avoid industrial hydrogen peroxide as it may not be prepared and stored in a food-safe way.

Some great places to look for hydrogen peroxide are:

  • Grocery stores: check the pharmacy section, or where cleaning products are stored.
  • Pharmacies: pharmacies often carry h202 for first aid. It’s a disinfectant that can be used on wounds. Often they’ll have a 3% strength solution out on the shelf, but you can get a 30% solution from behind the counter. The 30% strength is much more economical because you can dilute it and end up with way more product. Make sure it’s food-safe.
  • Health food stores: many health food stores carry hydrogen peroxide because it’s popular in the organic and health food communities for sterilizing fruits and vegetables.
  • Specialized suppliers: Different chemical, paint, and other industrial suppliers can carry hydrogen peroxide, but be careful that it’s produced in a food-safe way and mentions that on the label. Call the manufacturer if you’re not sure.

And no matter where you buy your hydrogen peroxide, make sure you use gloves and a face shield because it’s very reactive.

Read the label, and protect yourself.

Hydrogen peroxide will irritate and corrode your skin, and you should call your local emergency services if you get any of it in your eyes. Be careful with this stuff, especially if it’s 30% strength.

Smells sour or bad

There can be a lot of strange smells coming from microgreens, but there shouldn’t be. To diagnose a bad smell from your microgreens, you’ll need to get a little bit more specific:

  • Smells like rubber: If you’re growing hydroponically, and using grow mats or pads, you might smell something like rubber. This is from latex that’s used to bind grow mats together. Latex comes from natural sources, it’s a white milky secretion by a lot of plants, but it can also have additives like casein (a rubber softener separated from milk), which isn’t strictly vegan. It might smell funny, but it’s the growing media, and not your microgreens so the smell shouldn’t linger in your final product.
  • Smells sour: Toss your microgreens. Sour smells are often a result of bacteria, and there isn’t anything you can do to kill off bacteria and save microgreens. Bacteria are a huge concern for food-safety, and just not worth the risk. Throw out the whole tray.
  • Smells like sulfur: If you’re growing broccoli in particular, and some other brassicas, a slight sulfury smell is normal, especially when the microgreens have just germinated. Broccoli is high in extremely healthy sulfur compounds including sulforaphane, that are actively being studied for their wide range of suspected health benefits. Keep growing and enjoy.
  • Smells earthy: this is the best-case scenario. Healthy, happy microgreens should smell earthy and fresh, almost slightly sweet.

Microgreens have white fuzz on all of them

If there’s an even white fuzz growing from the roots of all of your microgreens you’re in luck! It’s not mold, it’s root cilia or fine hairs. These are little micro-roots, and are perfectly normal parts of your microgreens.

You can find more information on telling root hairs apart from mold in this article:

How do you Remove Mold from Microgreens? (Links to Article)

Microgreens are covered in mold

Mold is one of the biggest problems new and experienced growers run into. I still have the occasional problem with mold, and I’ve grown a lot of microgreens, so you’re not alone.

Microgreen is a symptom that can have a lot of different causes, but the two big ones are:

  • Starting with Mold: microbes left over from the last grow, on your trays or equipment, or improperly composted soil can be a big cause. You also might get a batch of seeds that wasn’t stored properly or just ended up having more mold spores for whatever reason. Properly sanitize and buy seed and soil that’s as sterile as possible.
  • Conditions: too much humidity and too little air circulation create the perfect conditions for mold. Increase air circulation by reducing seed density or installing fans to move air, or decrease the humidity in the air with a dehumidifier or watering less and from below (sub-irrigating) between trays.

To identify mold (and make sure it’s not root hairs) look for fuzz that isn’t pure white color, or spiderweb looking things crawling across your tray. Mold will usually start in one or more places and spread from there. If it’s an even white fuzz that’s emerging from all of your roots, then it’s probably normal root hairs (great photos and more info in the next two links).

Get more information on identifying, preventing and dealing with mold once you have it here:

How to keep microgreens from molding (Links to Article)

How do you remove mold from microgreens? (Links to Article)

Wilting: damping off

Damping-off is usually first visible as a thinning and darkening of the stems. Usually you first see it right where the stems are emerging from the soil. Then the microgreens wilt and fall over, or the leaves shrivel up or droop.

Damping off can be tough to pin down. It’s thought to be caused by fungi growing in the soil, that were introduced by your tools, the soil, the seeds, or blowing in on the wind. It could also be left-over on the trays from your last grow, making the case for sanitizing properly.

Damping-off microorganisms include:

  • Pythium
  • Fusarium
  • Rhizoctonia
  • And because of these little monsters (and others), when you’re growing microgreens you’re in race.

You want to promote growth of microgreens, and prevent ideal conditions for microorganisms.

If you continually have problems with damping off, eliminate the potential causes one by one:

  • Tools: Sterilize your tools and growing trays to the best of your ability
  • Soil: try a well-draining soil, a soilless mix, and source the most sanitary soil you can
  • Environment: grow inside instead of in your greenhouse
  • Seeds: maybe your batch was contaminated, try a new variety
  • Water: It’s unlikely, but your water source could be the problem. If you’re using rain barrels, well water, or otherwise untreated water, try switching as an experiment.

Stems are thin right above the soil and falling over

This is probably damping-off, a fungal problem. The troubleshooting guide right above this for Wilting: damping-off will get you off on the right foot.

Microgreens too wet when harvested

Too much moisture in harvested microgreens shortens shelf-life in the fridge, promotes mold growth, and is definitely something you want to avoid. You want your microgreens as hydrated as possible when they’re harvested, but not wet.

Microgreens are often wetter in the middle of the tray than around the edges. Some solutions for wet greens are:

  • Adjust the watering schedule, too much watering can increase evapotranspiration
  • Growing in greenhouse: consider growing indoors, or moving your microgreens indoors for a day or two before harvesting. It’s really hard to drive humidity levels down inside a greenhouse, even in more arid climates.
  • Seeding more densely around the edges and slightly less densely in the middle. The middle of the tray is usually where mold and other humidity problems manifest, so tweaking the seeding pattern can help.
  • Increasing ventilation or adding a dehumidifier can make sense once you’re growing a lot of greens, but the trade-off is increased power use, and more noise. I really like a brand of fans called Noctua, they’re designed for computers, but you can use them for other things if you’re handy with electronics. If you just buy the fan you’ll also need some way to power it, so it’s not the simplest thing to setup, and you’ll want to do it properly to keep everything safe.

Delivered greens wilting

If you’re not home when your microgreens are delivered, or you’re delivering microgreens to a customer, your greens are at risk of wilting!

Don’t just leave them outside the door unprotected. Give them a good knock and a phone call just to make sure no-one’s home, but the best backup is to put them in a cooler.

You might consider gifting an affordable cooler to your best customers for Christmas or as a surprise gift, but you can also ask them to place their own cooler outside the door.

If microgreens are too hot, or too cold in northern climates, they can wilt quickly.

This gives you a lot of flexibility in your delivering schedule too, so it can be a good idea to train your customers to get in the habit of putting out a cooler every Monday or whenever you do your deliveries.

But don’t overlook the benefits of some face-to-face time with your customers. Ask them how they like the product, how it’s keeping in the fridge, and maybe even set up a little referral program and mention how they can get some free microgreens if they sign up a friend or two.

Microgreens falling over

This is probably caused by too little water. When greens start to dry out slightly they fall over.

But there are a lot of other potential causes:

  • Seeding density: Another cause can be low planting density. Physical support happens when the plants are close enough to touch. Try increasing your planting density slightly.
  • Tray depth: If you consistently have greens falling over, you can also try a 2” deep tray instead of 1”. With a 2” deep tray, the trade-off is that harvesting won’t be as easy. You may need to lift the microgreens, roots and all, out of the tray to cut your microgreens off down close to the soil, unless you’re using 2” of soil, but then your 2” deep container isn’t supporting your microgreens. I’d recommend sticking with a 1” tray, and watering a little more frequently or tweaking your seeding density.
  • Thin stems: thin stemmed microgreens dry out a lot quicker, and can wilt easily.
  • Disease: mold can cause microgreens to shrivel up right above the soil-line (damping-off), tweak watering, humidity, and ventilation, or seeding density.

I go into a ton of detail, root causes, and solutions in this article:

11 Reasons why Microgreens Wilt and Fall over (And How to Save Them)

Don’t have a lot of light (ex: in a basement)

If you’re growing in a low-light apartment or in a basement you’ll need to add supplemental light. It can be a good idea to add artificial lighting even if you’re growing in a well-lit area, because even bright seeming rooms are a lot dimmer than sunlight that plants are used to.

Direct sunlight can be 100000 lux (a unit of brightness) in direct light, and 20,000 lux if you’re outdoors in the shade. Near a bright window or under concentrated task lighting you might get 1000 lux, typical indoor lighting is around 100-300 lux.

So that’s a huge difference!

But fortunately, microgreens are very tolerant of different lightings, so as long as they’re getting some bright light, and it’s not tungsten or incandescent light, they’ll be fine.

I would go for LED lighting, you can find a lot of great options online (and also some bad ones), check out my recommendations in my lighting buyer’s guide.

Green microgreens turning yellow

If your microgreens were green, and then turned yellow, something is wrong. This isn’t an issue I’ve run into on a large scale, I’ve just had one or two microgreens turn yellow.

Microgreens don’t usually grow for long enough to run into a lot of the issues that might cause leaves to turn yellow on other plants, my article on yellow orchid leaves has a good discussion of causes of yellowing, and whether or not you would expect the leaves to come back.

But for microgreens, they get most of their energy and nutrients from the seed, so if they’re turning yellow I would look for:

  • Changes in light, did you move your grow tray further from light?
  • Longer than normal blackout period
  • Mold or insects attacking the roots
  • Water pH: non-neutral water (lower than 5 or higher than 7.5 pH) can prevent nutrient uptake, but for quick growing microgreens it shouldn’t have time to drastically affect the microgreens

Keep in mind that some microgreens are bred to look yellow, they might have yellow veins on their leaves, or yellow stems, and popcorn shoots are grown 100% in the dark, so they’re yellow on purpose too.

I don’t really have a good answer for why microgreens turn yellow, but I did a little bit of investigating and took some neat photos and posted them here:

Why do Microgreens & Seedlings Turn Yellow? (Links to Article)

Microgreens not turning green

Microgreens never turning green is likely because they didn’t get enough light soon enough. If they’re wilting it’s from not enough water/humidity, but staying yellow is probably a light issue.

Move the microgreens to brighter light, your blackout period may also have been too long.

And keep in mind that some microgreens are supposed to look yellow (like popcorn shoots, and yellow beets).

Stunted Growth

Stunted growth for microgreens can from a few difference causes, most commonly:

  • Not enough light
  • Not enough UV light

For other plants stunted growth is often a nutrient deficiency, but because microgreens rely heavily on the nutrients in the seed, and don’t grow for very long (typically 1-3 weeks, nutrient deficiencies are unlikely to stunt growth.

Yellow stretching stems

If your microgreens are stretching (long stems) and have a yellow tint, it might mean they spent too long in the dark, in the blackout period. The blackout period is great for ensuring even germination, it keeps everything really moist and in contact with the soil, but it’s a race against time.

The seeds only have so much energy, and they’re spending a little bit of it every hour. After a long blackout periods, they might be completely drained of energy and nutrients, and take a while to bounce back, which could result in yellow stretching stems.

The reason they’re yellow and leggy (stretching) is that they’re reaching out for light. When plants don’t have enough light, they’ll often stretch towards the light source. If your microgreens are yellow or have longer stems than you want, your light source might not be bright enough.

They expend energy growing and searching for light, and if they don’t find it quickly enough they’ll weaken, wilt and fall over.

Microgreens won’t regrow after cutting

A lot of different types of plants are lumped into the term microgreens. Not all of them are true microgreens. Pea shoots and popcorn shoots (young corn) are two examples. These are actually shoots, which grow in a different way from most microgreens.

Shoots can be harvested more than once because they don’t have cotyledons that you’re cutting off. The seed stays down near the soil, and send up a shoot. And usually, as long as you leave at least one little leaf below where you cut, you can get multiple harvests.

But don’t re-grow corn, it will be too tough and bitter. Peas are great for a second cut.

Most microgreens (broccoli, mustards, radishes, sunflower) won’t regrow. Or at least not much, you might get a few of the slower germinating seeds popping up, but mold and pathogens will have that much longer to catch up.

Not enough space

At first you might look around your home or apartment and think you have no room to grow microgreens. Greenhouses are really expensive and take up valuable real-estate. Some of the best rooms in the house are the ones with big windows, so where can you grow microgreens? There just isn’t enough space!

Well actually, you can grow microgreens almost anywhere indoors. The standard 10” x 20” greenhouse flats can be placed on shelves. A single shelving unit can fit up to 16 trays, way more than enough for a large family that eats a lot of greens, and it can fit in as little as 6 square feet. 

Smaller containers can go on windowsills, you can grow microgreens in just about any container (although perforated ones with drainage holes are best). Watch out for cool drafts if you’re in a more northern climate, and too much sun can be a problem if it’s really hot too. 

If you’d rather avoid windows, you can grow your microgreens under lights (this is what I do). It lets you get a really consistent lighting, and then you can really grow your microgreens anywhere, even in a basement. LEDs are cheaper than ever, and last decades. A 4-foot LED Strip can light four 10” x 20” trays, although two 4-foot LED Strips is better. 

Slow growth

Some microgreens grow in as soon as 5-7 days including germination, but some take longer, a lot longer. Basil can take up to 4 weeks depending on the variety.

So before you get worried that microgreens are growing slowly you need to make sure they’re not just a slower growing species. Some of the slowest growing microgreens are:

  • Basil
  • Chard
  • Carrot
  • Amaranth
  • Fennel
  • Beets

If you’re having slow growth with typically faster growing microgreens, it could be a few different things:

  • Seeds: extremely fresh seeds may still be dormant, they can take a little while to germinate when they’re very fresh. Older seeds can lose vigor and viability and germinate slowly and unevenly too. Ask your seed supplier about your specific batch. Or if you bought them a long time ago, they might just be past their prime. Consider storing seeds in an airtight container in the fridge or freezer.
  • Watering too little can also slow growth. Microgreens need a good balance of water and light to get growing. Also if you’re skipping the blackout period, that can slow growth too. The blackout period serves to even out the germination through evenly hydrating the seeds and providing optimal conditions for them to get started.

Can’t tell if microgreens are organic

When you’re shopping for microgreens at the store it can be hard to tell exactly what’s organic. Even if the microgreens are in the organic section, they might not be. They also could be marked with any of the following:

  • Pesticide and Herbicide free
  • Grown with Organic Seeds
  • Certified Organic

You can find tons more information on organic microgreens here:

Are Microgreens Organic? It Surprised me to Learn… (Links to Article)

Harvesting takes too long

It seems simple, but there are a lot of ways you can speed up your harvesting and get more of your microgreens on your plate and less on the floor.

For everything I know about harvesting read more here:

Harvesting Microgreens: The Ultimate Guide (When, How, and Top Tips) (Links to Article)

And for my recommended harvesting equipment, I set up this page:

Harvesting Equipment Buyer’s Guide

Seeding takes too long

Spreading seeds can take a long time when you start growing more trays. I still spread seeds by hand using a simple container (I actually use a pop bottle cut in half). If you want to take things to the next level you have a few options.

There are seed spreaders that are basically giant salt shakers. But I find that they don’t really make things any easier, you might have better results. 

There are also seeding plates. They’re basically a two layered perforated plate system. The seeds get trapped in little holes, then you brush off the extra seed, then you shift the bottom plate to align the holes and the seeds fall on to your tray, perfectly spaced. 

It’s the commercial way to do it if you’re at a huge scale, but not something I’ve tried myself.

Less growth around the edges of tray

It’s normal for your microgreen canopy to curve downwards towards the edges. Almost like a loaf of bread. 

But if it’s extreme, your trays are probably drying out. They dry out near the edges first, because the middle of the tray traps moisture. If your microgreens are wilting and falling over at all near the edges, that’s another sign that you likely should be watering a little more. It could also be from extreme heat but it’s usually under-watering in my experience.

Trays are Cracked

Cracked trays are really annoying, but I don’t have to tell you that. Maybe you dropped one, even just a few feet and it cracked.

They can be tricky to fix, but a quick way to go about it is to use a specially formulated glue, or a special tape. I’m not sure about the food safety of the glue however, so I’d lean towards upgrading to better trays as soon as possible. 

There are other ways to fix plastics, like melting the pieces back together, or gluing patches on, but it’s just not worth the trouble for cheap greenhouse trays.

The other option, which is more sustainable in the long-run is to buy high quality trays. If you’ve worn out or cracked a set of cheap ones, you can probably justify upgrading to something that will last the rest of your life. I walk through my recommended trays here.

Trays are too flexible, I dropped my growing microgreens all over the floor

Flexibility of trays can be a good thing, the more flexible they are, the less likely they are to crack, unless they’re very thing. But if your trays are too flexible and it’s causing you problems in your grows, you have two solutions

  • Buy trays that are more rigid, there are many manufacturers that have recognized that low quality disposable trays were a huge opportunity to improve on. More rigid trays are also a lot more durable and made of better materials in a lot of cases.
  • Grow with nested trays (perforated inside solid), this adds the rigidity of two trays together.

If you want a suggestion for the grow trays I use, check out my page here where I get into more detail:

 Growing Tray Buyer’s Guide (Links to Article) 

Uneven Growth from one end of tray to the other

This is actually a problem I ran into recently. I was consistently getting higher growth on one end of my trays than others. At first I was convinced there was extra light coming from one side, but what it ended up being was that the shelf wasn’t level!

With an un-levelled shelf your trays sit on a slight angle. If you’re watering between a solid and perforated tray (sub-irrigating), the water sits in the bottom tray for a little while as it’s soaked up into the soil. If it’s off-level, one side is always a little wetter, and the other is always a little slower. 

Check your shelves or growing surface when you first set it up and makes sure everything is level!

Dead patches/patchy growth

Patchy growth means your soil and seeds are going to waste, so it’s a problem you’ll want to troubleshoot quickly. Uneven seeding or too much seed are the likely causes. It could also be clumpy soil, or mold.

Spreading seeds evenly, and at the right density will give you much higher yields. Too much seed can actually reduce the amount of microgreens you get because some seeds will actually kill nearby seeds. They can secrete natural herbicides in a phenomenon known as allelopathy. The evolutionary benefit is thought to be that it gives any one seed the best chance of germinating if it lands near a bunch of seeds of another species and wipes them out.

Luckily the natural bio-herbicides don’t spread very far, so with even seeding you’re in good shape.

Clumpy soil forces seeds together in the low spots. Press soil down with something flat to smooth out some of the clumps, or run it through a soil screen or sieve. 

Look for mold growth near the dead patches. More on mold prevent here and telling mold apart from root hairs here.

How to keep microgreens from molding (Links to Article)

How do you remove mold from microgreens? (Links to Article)

If there’s mold, you’ll want to make changes to your seeding density (lower it), humidity (lower it), or increase ventilation. It could also be contaminations in the seeds or soil.

Bitter flavor

A lot of microgreens become more bitter as they mature. A big case-in-point are sunflower microgreens. The taste rapidly gets bitter once they start to sprout the first true leaves.

Golden popcorn shoots can become bitter if they’re exposed to light and allowed the green. That’s why they’re grown as yellow shoots and not as microgreens.

Some fertilizer can impart an off-flavor to microgreens. Avoid fish-emulsion and any un-composted manures for microgreens, even if you’re growing outside.

It could also be the variety of seed. Microgreen seeds may be specially selected for tender and delicious young microgreens. If you’re not satisfied with the flavor it could be the seeds.

In worst case scenario, you may also be using non sprouting/microgreen safe seeds that aren’t marketed for human consumption. They may have fungicides, herbicides, pesticides and other residues. These can splash up if you’re watering from above (another reason to sub-irrigate), and get on the stems and leaves and alter the flavor.

Going bad quickly in the fridge

If you just bought some microgreens, or grew them yourself, quick spoilage is due to:

  • Storing in perforated containers is the number 1 microgreen killer across the nation. Perforated containers let you microgreen’s moisture escape. Microgreens last longest when they’re stored in high humidity, low temperature, and no standing water. Store microgreens in a
  • A dirty fridge. Clean your fridge and sanitize it with bleach, rubbing alcohol, hydrogen peroxide, vinegar, or something antimicrobial. Biofilms build up in the humid environment of your fridge, and it’s crawling with microbes.
  • Harvesting way before consumption. Some microgreens go through distributor warehouse for a few days, and then sit on the shelf in store for up to a week after that. By the time you get them home they could have been harvested a week or more previously. Harvest right before you eat them, or if you’re buying, try to buy right from the source.
  • Ceramic blades are said to keep the cut ends cleaner, something to do with ion exchange. I haven’t looked into it, but I’ll try some experiments once I get my hands on some ceramic scissors.

I put together a surprising amount of information on storing microgreens properly here:

How to Store Microgreens After Harvest & Maximize Shelf Life (Links to Article)


Wow, even if you just scrolled down to the bottom, that’s a lot of work!

There are a lot of things that can go wrong with microgreens but the majority fall into one of the following categories:

  • Water: humidity too high or low, too much or too little watering, or pH issues
  • Disease: pathogens, often fungi (mold) and bacteria can cause wilting, uneven growth, and damping-off. Sanitize and buy the most sterile tools and seeds possible.
  • Lighting: the right blackout period, and even lighting can solve a lot of problems. Follow the right steps, and buy the right lights and you’ll be in good shape.

If you found this article useful, one of the biggest ways you can support me and keep the content flowing is to share this article with a friend or two. It makes a huge difference!

Good luck, and keep at it!

We need more microgreens on this planet.

Next steps 

Brush up on the key steps and double check you’re not missing anything if you’re an experienced grower:

How to Grow Microgreens in 11 Easy Steps (Updated 2020) (Links to Article)

And if you want to upgrade your equipment to get the healthiest most consistent harvests, and drive down soil and seed costs, check out my recommended supplies here:

Equipment and supply recommendations 


I’m Alex Lafreniere. I learned a lot about plants when I built and operated a landscaping company. I learned even more when I started growing and selling Microgreens. But, learning is a journey, not a goal. Ever since travelling across the world, I’ve wanted to find ways to bring more delicious and exotic plants into my life. This is the site where I share everything I’ve learned with you. And maybe we’ll learn a thing or two together.



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