I don’t know anyone that likes to get sick.

When you first start experimenting with microgreens, you’ll probably grow a tray (or maybe ten) that have mold! It’s inevitable that you get thinking about food safety and maybe you start to wonder if microgreens are a good idea at all.

Microgreens are generally safe to eat raw if grown properly. Microgreens can make you sick through food-borne illness if: improper seed is used (with pesticides, fungicides, or coatings), improper growing conditions lead to mold growth, unsafe food-handling practices introduce pathogens.

This could be through cross-contamination with animal products (commonly raw chicken, eggs, or meat) that contain Salmonella or E-coli.

Disclaimer: take any information here as general guidance only, you should familiarize yourself with your local rules and regulations, and follow them if there’s any disagreement with what you find here.

Fortunately, while microgreens can make you sick, there is a lot you can do to reduce the chances to almost zero by following good food-safe handling and growing practices.

Most food-safe practices are common to all foods, but there is another layer of depth when you’re growing microgreens that we’ll get into in more detail below.

Are Raw Microgreens Safe to Eat?

Raw microgreens, just like any other vegetable, are safe to eat if they’re grown, handled, and processed properly. Microgreens (and sprouts) need to be grown in a deliberate and careful way to avoid food borne illness through pathogen growth.

The big risks to your safety when eating raw microgreens are Salmonella (Salmonella enterica and Salmonella bongori), E.Coli (Escherichia Coli 0157 H7), and various molds (fungi).

Perfectly pure microgreens, grown in a magical microorganism free alternate dimension are safe to eat raw. But in the real world we have to consider the invisible micro-biome and account for it in growing, harvesting, and food preparation methods.

Are Microgreens Safer than Sprouts?

Microgreens are safer than sprouts because you’re not eating the roots which are in contact with the soil where the majority of pathogens live, and you can grow them in less humid and cooler conditions which aren’t as ideal for pathogen growth.

How to Grow Safe Microgreens that Won’t Make you Sick

When you’re growing microgreens you want to promote fast strong microgreen growth, and do everything you can to prevent contamination and ideal conditions for pathogens.

To do this you need to focus on two things: keeping humidity down, and avoiding soil contact with the foliage.

Keeping humidity down means lowering the amount of moisture in the air around your microgreens. When humidity is too high near the stems and leaves, the naturally present microorganisms that are floating around in the air, and in dust can take hold. Humidity and the right temperatures provides an ideal condition for them to quickly multiple.

There are a lot of factors involved in controlling humidity, but the most important are:

  • Get your seeding density right (too close and you trap in moisture and promote growth of mold and other pathogens)
  • Have adequate airflow, especially if the humidity in your area is high, like down closer to sea level. You can also install a dehumidifier in your grow room. Seeding density helps with this too.
  • Don’t water too much, overwatering causes more moisture to evaporate from the soil, and causes the microgreens to evapo-transpire at a higher rate

Avoiding Soil contact with foliage & stems is important because soil is a moist, protected environment for pathogens to grow, and provides all the nutrients they need. Even high quality soil is something you don’t want to eat, so don’t let it get on your food if you can avoid it.

To keep soil off you greens while you grow, keep the following factors in mind:

  • Burying your seeds under a layer of soil will cause all your cotyledons and stems to push through soil as they grow. This means any seed hulls that shed above the soil line (like sunflower) will have more soil on them and be more likely to be contaminated.
  • Be careful when you harvest. Harvest so that you’re not getting soil on your scissors, knife, or other harvesting tools. If you do, you’ll transfer the microbes from the soil to every microgreen you harvest, unless you carefully sanitize your tools.

And as an added precaution, wash your greens before you eat them under clear flowing water. This can rinse microorganisms off the surface and is recommended universally.

It’s a good idea to wash right before you eat (not at harvest), because washing tender microgreens can damage the natural protective layers they have.

I’ve found that the additional handling and micro-damage that happens to the surface of the greens causes them to wilt and spoil faster if they’re washed right after harvest. Although if there’s visible soil on your microgreens after you harvest, you should rinse it off right away.

Another important thing to do is to get your microgreens into the fridge as soon after harvesting as possible. This slows decomposition and helps slow metabolic activity, reducing how much moisture they’re losing.

What are the Typical Food Borne Illness Pathogens?

Food-borne illnesses have a few usual suspects that cause problems. Fortunately we only need to worry about a few of them in the case of microgreens.

Bacillus Cereus

A bacteria that can produce spores and toxins that survive normal cooking and reheating, making it dangerous, even after exposure to heat. This bacteria can contaminate a wide range of foods, it’s not a common food borne illness in fresh produce.

You can slow this one down by keeping food below 40 F (4C). This is also something you should be doing anyways. Getting the field-heat (or shelf heat) off microgreens as soon as you harvest by putting them into a fridge or cooler is a critical step in extending microgreen life and keeping the quality high.

E. Coli (Escherichia Coli 0157 H7)

E coli has caused a lot of problems for a lot of people. It’s interesting, but something I found out when refreshing my food-safety courses is that most E. coli strains are completely harmless. It’s the 0157:H7 that is most serious and does a lot of the damage.

E. Coli is a bacteria that’s a main concern for microgreen growers.

E. Coli can contaminate vegetables, milk, meat and a lot of other things. The recommendation by the health agencies in my area are to wash fruits and vegetables under clean, clear running water. The idea is to flush the bacteria off the surface. You’ll want to double check the regulations in your area if you’re selling microgreens, and it’s probably not a bad idea even if you’re growing for yourself and your family.

Salmonella enterica & bongori

Salmonella is another common food-borne bacteria that’s harmful to humans (a pathogen). Salmonella has some nasty symptoms, and can actually cause arthritis as soon as one month after a person is infected. It usually contaminates chicken and eggs, but can be in vegetables, greens, and almost any food, even processed food.

Be especially careful when washing, cutting, or handling poultry in your kitchen. If you rinse poultry or meat in the sink, be careful that you don’t splash Salmonella and other pathogens all over your kitchen. If you do, it’s a good idea to sterilize everything afterwards with H202 or another sanitizing agent (vinegar isn’t reliable).

“The effect of hydrogen peroxide on Salmonella typhimurium in whole egg was evaluated. The bactericidal effects observed on the test organism at 5 degrees and 20 degrees C were found to be similar. There was a 99% kill in the presence of 0.5% and 1.0% H2O2. Addition of the test organism and H2O2 after pre-heating the egg material at 40 degrees C for 15 min caused a rapid kill which was 10,000-fold greater than that produced by H2O2 alone.“


Staphylococcus Aureus

This is one of the bacteria that is naturally found on our bodies. It’s often in our respiratory tract, and on our skin. This bacteria can easily contaminate food, where it spreads and grows unchecked to dangerous levels.

When it’s growing in food it can create toxins that don’t break down with normal cooking, so this is a perfect example of why we need to wash our hands well with soap and water when preparing or handling food. Another precaution is not to touch your face or hair while preparing food.

In commercial settings a hair net, fancy chef’s hat, or some way of tying hair back and out of the way is also a good idea.


Pathogens certainly aren’t limited to bacteria. Norovirus is a virus and the number one cause of vomiting and diarrhea. It’s a very resilient infectious agent that’s not killed by some hand sanitizers and some disinfectants. But soapy water and good hand-washing technique reduces it to safe levels on our hands.

We’ve taken a quick dive into the 5 most common food-borne illness pathogens to get an idea of why some of the food safe practices make sense. When preparing microgreens, wash your hands, sanitize any surfaces that come into contact with meat (or spray), and do everything you can to avoid cross-contamination.

If you take the above steps, you’ll significantly reduce your chances of getting sick.

What Kinds of Microgreens can Make you Sick without Pathogens?

Some microgreens can make you sick if you eat large quantities, even if the microgreens are free of dangerous levels of pathogens.

Buckwheat (Fagopyrum Esculentum)

  • Fagopyrin is present in buckwheat vegetation (but not the seeds). It’s a pigment that reacts with ultraviolet light, and can cause photosensitivity in un-pigmented skin, potentially damaging blood vessels, cell death, and sloughing of skin. Small quantities of buckwheat microgreens likely won’t cause issues for most people, but I don’t grow it because of the added risk. https://en.wikipedia.org/wiki/Fagopyrin

Quinoa (Chenopodium Quinoa)

  • Quinoa contains saponins, a bitter family of chemicals that lather up like soap! The bitter taste is thought to keep pests at bay, they don’t like the taste either. Eating large quantities of anything very bitter can cause stomach upset, but I haven’t found good evidence that saponins are something that should be avoided when selecting which microgreens to grow and eat. Especially because they’re easy to detect by taste.
  • Saponins also have a lot of health benefits:

“Saponins, affect the immune system in ways that help to protect the human body against cancers, and also lower cholesterol levels. Saponins decrease blood lipids, lower cancer risks, and lower blood glucose response.”


Alfalfa (Medicago sativa)

  • Alfalfa microgreens contain saponins as well, just like Quinoa, but they also contain Lectins and Canavanine. Some people will get sick from saponins if they eat large quantities.
  • Lectins are a family of proteins that are in almost everything we eat, especially grains and legumes like peas and beans. Some lectins are toxic, but cooking gets rid of even those. Jacalyn See, clinical dietitian at Mayo Clinic recommends that: “we shouldn’t eliminate this nutritious carbohydrate-binding protein from our diet”.
  • Canavanine is another chemical that plants produce to defend against pests. The quantities of it in Alfalfa aren’t enough to cause problems.

Can Microgreens give me Food Poisoning?

Any food can give you food poisoning, it depends on how it has been grown, handled, and stored. Microgreens grown with proper seed, in sanitary containers, with properly composted soil, and harvested with clean equipment are safe to eat.

But you’ll also need to make sure they’re stored properly at food-safe temperatures below the danger zone (40°F/4°C).

Then when it’s time to prepare your microgreens, you need to use clean utensils and cutting boards and avoid cross-contamination.

If you managed all of the steps above, microgreens won’t give you food poisoning.

What is food poisoning? Foodborne illness is another word for food poisoning. And it’s caused by consuming food and beverages that are contaminated with pathogens, or the toxins that those pathogens have produced (which can stick around even after you’ve killed the pathogens that created them).

Pathogens of all types can cause foodborne illnesses: parasites, molds, bacteria, and viruses.

Food poisoning can have some nasty symptoms ranging from mild to serious illness and a whole range of nasty symptoms (Diarrhea, vomiting, nausea… the list goes on.) More serious problems can develop in some cases, and they can be life threatening: Kidney disease, liver disease, paralysis, and even death.

And unfortunately we’re all at the mercy of food-borne pathogens, anyone can get sick from improperly grown, stored, or prepared food. There’s no way to build up an immunity to all of the food borne illnesses. Certain populations are at higher risk, including:

  • Compromised immune systems
  • The elderly
  • Pregnant women
  • Babies and very young children
  • People with other health complications suck as other illnesses

Steps to reduce the chance of getting sick from Microgreens

How to protect against foodborne illness takes a multipronged approach. You need to educate yourself first, and then those around you including your family and coworkers

  • Keep foods below 40°F/4°C or above 140°F/60 °C (the danger zone)
  • Clean and then sanitize working areas, surface, equipment and tools
  • Wash your hands with warm water and soap
  • Store and prepare food safely and avoid cross contamination
  • Internal temperature: know the minimum internal temperatures for the food s you prepare, print a table of them and keep it in a nearby drawer if you’re unsure or put it on a wall
  • Cool and reheat food quickly to reduce time spent in the danger zone

Microgreen Spoilage Germs vs Pathogens

When I first learned about this concept, it blew my mind.

It’s obvious that It’s not always apparent that there is something wrong with the food you’re eating, otherwise you wouldn’t eat it, but really thinking about it, this has some deep implications.

There are two general classifications of germs. Pathogens (the ones that make you sick), and spoilage germs (the ones that spoil the look, smell, and taste of your food). Most pathogens don’t give food a bad taste or smell.

We usually think of food safety more for meat and fish, but the same principles are really important for produce too.

Food that has been well cooked can still make you sick! Just because you cooked it doesn’t mean all the pathogens were killed. Leaving out the cooked food can allow the remaining pathogens to multiply, and then the next time you take a bite you could become ill.

Food poisoning doesn’t set in immediately! In the case of Listeria It can take up to three weeks before symptoms present in some cases. For some foods though it’s relatively quicker, within a day.

Most Pathogens like Salmonella and E Coli will not die in the freezer. Even frozen contaminated foods like frozen chicken will contaminate anything it touches.

Vinegar isn’t a reliable sanitizer for killing germs. Commercial kitchens are required to sanitize using approved substances at approved concentrations. For my area its bleach above 100ppm, quaternary ammonium compound above 200 ppm, or iodine at 12.5 to 25 ppm.

Steps to Keep Workers Food-Safe

If you’re selling microgreens you have a whole new set of problems and responsibilities: you need to share everything you know with your workers.

Building food safety into your processes and company policies is critical for making sure you have a work safe environment.

On top of what we’ve discussed above, keep the following in mind if you’re growing commercially:

  • Workers (including yourself!) can be contagious of food borne illnesses weeks before and after having symptoms, so you need to practice good hygiene even if everyone appears healthy.
  • Don’t let workers work with food if they’re sick (check your local regulations, but err on the safe side)
  • Make sure employees are showered and wearing clean clothes
  • Inspect nails for grime and make nailbrushes available so they can give their hands a good scrub if they’re not wearing gloves.
  • Control hair and tie it back so it doesn’t move. Moving hair increases the chance it will fall into the food


Most microgreens won’t make you sick, but only if they’re grown properly with the right supplies, handled properly, and stored properly.

Microgreens can harbor a lot of different pathogens, so take food safety seriously, and follow the guidelines laid out by your government regulatory bodies.

Buy seeds marketed for sprouts and microgreens as they’re held to a higher standard, use properly composted soil, and clean and sanitize all your growing equipment between crops.

Make sure harvesting tools are sanitized too, and get your food into a food safe temperature (below 40F/4C) right after harvesting.



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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