It is really disappointing to germinate seeds for sprouts, or get them home from the market, only to find out they have a smell.

A bad smell.

The smell is usually because something other than your sprouts are growing: sprouting conditions are really ideal for microbes.

Why do my sprouts smell bad?

Sprouts smell off or rancid because the humid conditions for sprouting encourage bacteria and fungi to grow, and these release compounds with nasty smells. Rinse thoroughly and prevent any standing water to prevent bad smells. Learn more below. 

So it’s a constant battle to give your sprouts the edge through good timing, frequent rinsing, and using top quality & clean seeds, water and equipment. (Wow that’s a mouthful).

Here are some contributing factors and possible explanations for why your sprouts smell bad:

  • The initial soak was too long
  • Drainage problems: Too much water remained with the seeds
  • Didn’t rinse frequently enough
  • Used unclean water, or water unsuitably high in chlorine, salt, or other contaminants
  • Unclean equipment: Your sprouting jars or other equipment isn’t clean enough. Sterilize in boiling water for great results.
  • Purchased Sprouts: They were bad when you bought them
  • Insect Problems: make sure fruit flies and other critters can get at your sprouts.
  • Bad Seeds might be from a high pathogen source, or they were improperly stored. Some seeds are labelled pathogen free.
  • Fungicides that aren’t safe for humans might be present on some seeds that aren’t specifically marketed for sprouts, some of them have a smell.
  • Unskimmed floating seeds, fragmented seed hulls, and other debris

It could also be that you’re growing broccoli sprouts, and you’re just not used to the smell. Broccoli contains glucoraphanin (which breaks down into sulforaphane) and other compounds that have a bit of a sulfur smell, like cabbage.

Are broccoli sprouts supposed to smell bad?

Broccoli sprouts have a distinct smell. Some people describe it as a sulfur smell. Once you’re familiar with the smell it’s easy to identify if the scent of broccoli sprouts are normal.

Some seed vendors recommend sprinkling a little bit of citric acid on the microgreen sprouts after a few days. This helps combat the unusual smell and makes them more appealing to sensitive and discerning palates.

One of the more unique compounds in broccoli sprouts is glucoraphanin. Glucoraphanin is thought to provide a huge number of health benefits, but has a strange taste when it breaks down into sulforaphane.

It’s one of those compounds that has a taste to some people, but has no taste to others.

Cilantro has similar chemical compounds in it, it tastes delicious to some, and like soap to others.  

How to tell if sprouts have gone bad or if they’re safe to eat?

It’s important to be able to tell when a sprout isn’t safe to eat.

Eating bad sprouts can expose you to Ecoli, Listeria and Salmonella, causing bad health problems, particularly to higher risk demographics like young children, the elderly and immunocompromised people.

Any rotten food is not good to eat. Sprouts and Microgreens are no different on this point.

There are three main ways to tell microgreens have gone bad:

The Smell Should be Fresh and Delicious

Pick up a fresh pack from the supermarket, and chances are they’ll have the proper smell.

Any other smell that’s slightly off, rotten, or unusual it’s not worth risking it. Any off smell is a good reason to throw your sprouts away.

The sprouts might look 100% fine, but if the smell isn’t right it is a sign that decomposition and unwanted microbial growth is occurring.

The Look, Sprouts Should Look Crispy, Firm, and Fresh

The colors should be bright, and usually white. Colors can be purple, green, yellow or other colors, but they usually have a lot of white. There are some great communities online where you could post a few quick photos and get an answer pretty quick if things look good or not.

Over time you’ll become familiar with how sprouts are supposed to look, and you’ll be able to quickly tell healthy sprouts apart from bad sprouts just from the look of them.

Another important point is to make sure it’s actually mold you’re dealing with, and not root hairs! This is such a common mix-up that I wrote an article about it that you can find here:

Microgreen Mold vs Roots: An Illustrated Guide to Telling the Difference (links to article)

Over time sprouts will lose some of their whiteness and develop a more amber and yellow color, this is somtimes called rusting. It’s usually fine at first, but your sprouts are really close to going bad. This can be a cause for concern, so make sure the scent is fresh if you’re going to eat them anyways.

Where you sourced your seeds from

The seeds: sourcing from a reputable source, that’s well certified, that you’ve had success with in the past, and handling them properly can give you increased confidence that your sprout seeds are good for sprouts.

Sprout seeds need to be fresh, untreated with fungicides, and stored properly.

There are a lot of suppliers out there that you can try if you have bad results. Make sure your sprout seeds don’t have any pesticides, this is even more important for sprouts than microgreens because you’re eating the whole seed and root with sprouts.

Why do my microgreens smell like a swamp?

Microgreens just like sprouts should smell crisp, fresh, and appealing. If your microgreens smell like a swamp you may have problems with bacteria, mold, or other microbes.

There is a slight smell to moist soil, and germinating seeds, but anything over-powering or evoking memories of swamp smells is cause for concern.

You problem could be from a few different things, but the most likely cause is microbial growth, probably bacteria and mold. This could be due to high humidity, standing water, poor airflow, contaminated seeds, or a combination.

To find out more about dealing with mold on your microgreens once you have it, check out this article:


To find out more about preventing mold from taking hold on microgreens in the first place, this is your resource:


Okay, so what’s the best way to sterilize seeds?

You’ve worked up a good plan for soaking and rinsing to keep your sprouts nice and fresh, and give them an edge against microbres.

And, you’ve got your tools and sprouting equipment nice and clean and sterile.

But, what’s the best way to sterilize seeds?

Household bleach is not safe for human consumption. So that’s out.

But there is another great option:

The University of California Division of Agriculture and Natural Resources has some key recommendation for sprout best practices:


” 1. Buy certified (pathogen-free) seed* AND

2. Treat the seed by heating on the stovetop for five minutes in a solution of 3% hydrogen peroxide (available at most drug stores) preheated to 140°F (60°C). 

3. Rinse the seed in running tap water for 1 minute… Then carefully skim off all floating seed, seed coat fragments, and other debris and dispose of them. Although skimming can be a tedious process, research has tied most contamination to these materials.” – Source


Related Questions

Why do my coconut fiber mats smell like feet?

Growing microgreens in coconut fiber mats can cause some strange smells. Some mats are held together by latex, rubbers, and other adhesives. These adhesives can cause some pretty powerful smells in an enclosed area.

Sometimes the mats have a liner, this liner can smell funny.

Coconut coir on its own doesn’t seem to have this problem, so it must be the adhesives and binding agents. It’s always worth some close scrutiny to make sure the smell isn’t coming from mold or other pathogens.


Alex Headshot

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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