Why Your Microgreens Smell or Have Mold & 6 Easy Fixes

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Moldy Microgreens

Are you experiencing a foul odor coming from your microgreens that you can’t quite ignore? This smell not only makes for an unpleasant growing experience but if you are a commercial microgreens grower, then the microgreens can’t be sold to customers. What a waste of microgreens!

So, why do the microgreens smell? Many reasons could be causing the microgreens to be smelling foul. Some of the reasons are root or stem rot, mold, humidity and temperature issues, and chemicals. All these problems relate to each other, and it’s vital to eliminate any possible cause for the production of healthy and tasty microgreens.

Here are six surefire ways to get your microgreens healthy and smelling great in no time:

  1. Lower the seed density.
  2. Avoid overwatering.
  3. Water from the right angles.
  4. Optimize the temperature and humidity.
  5. Eliminate mold.
  6. Sanitize the growing medium.

The main culprits of smelly microgreens are usually mistakes gardeners make that go unnoticed. In this article, we will discuss six practical ways to prevent microgreens from smelling and we will find out more about what makes them smell bad in the first place.

Practical Fixes to Smelly Microgreens

Smelly microgreens are a nuisance and they also bring huge losses in profit. To avoid growing smelly microgreens, here are the fixes you can implement:

1. Lower the Seed Density

If seeds are tightly clustered together, air deficiency and poor drainage occur. Some of the plants could grow, but they’ll end up being too congested. This could prompt root rot, which gives off terrible odors.

If you are having trouble with determining how much seed to put into your container, take a look at this great article from Home Microgreens – Seed Calculator.

2. Avoid Overwatering

Overwatering leads to the deficiency of oxygen and prompts root rot. But how much water is enough?

It’s simple. The soil or other growing media should be moist, not wet. Experiment with different moderate amounts to determine the most favorable levels. Use this Soil Moisture Sensor from our Best Garden Tools page to determine the optimal amount in a specific growing area.

Simply check the microgreen plants every day and water if necessary. A good water sprayer or a self-watering system might also help if you are still struggling. Check out our True Leaf Market Products page for some helpful links to affordable options!

3. Water from the Correct Angles

While it’s okay to water from the top when the seeds haven’t germinated, that’s not always the case for sprouted microgreens.

If microgreens have some leaves, start spraying water from the bottom. If plants are sprayed from the top, the dense stems will trap moisture and cause musty smells, which can escalate to plant rot.

4. Optimize Temperature and Humidity

In order to optimize temperature and humidity for microgreens, think about how this is accomplished in the home.

Humidification for plants occurs when they are watered. However, it is recommended to use a dehumidifier and an air fan to control humidity levels and promote aeration. Many microgreen farmers fail to optimize humidity and temperature, and it costs them big time. Be ahead of the game and grow fresh, smell-free microgreens.

5. Eliminate Mold

If mold is noticed that is making microgreens smelly, eradicate it before it spreads. Here are two ways to get rid of mold on microgreens:

  1. Make a weak mixture of water, white vinegar, and hydrogen peroxide to spray onto the plants.
  2. Place the microgreens in sunlight. Mold will dry up and die.

See how to remove and avoid mold from microgreens by following this advice from Urban Farmer Curtis Stone:

HOW TO: Avoid and Remedy Mould On Microgreens

6. Sanitize the Growing Medium

Microgreens might take in chemicals that lead to smells. To avoid this, ensure that the components of the growing medium are well researched.

Most organic microgreen growing pads are expensive. However, they are worth the price since they produce healthy, tasty greens with little issues when growing.

Also, use food-safe plastics to ensure no chemicals like lead from PVC are absorbed by microgreens to influence their smell.

So do not fear, for I am with you; do not be dismayed, for I am your God. I will strengthen you and help you; I will uphold you with my righteous right hand.

Isaiah 41:10

Why Your Microgreens Smell

Now that you’re aware of how to stop microgreens from smelling bad, it’s important to understand what causes microgreens to smell. Depending on set up, the microgreens could be experiencing any of the following issues.

Root or Stem Rot

Damping Off Seedlings

Root and stem rot can be caused by heat stress, high humidity and lack of ventilation. All these factors go hand in hand because high temperatures plus high relative humidity without consistent airflow lead to air deficiency.

Sometimes, root rot is also caused by damping-off — a disease that’s more prevalent in wet conditions.

If a swampy smell is noticed, then inspect the set up immediately. Roots or stems will begin rotting if the issue is not remedied quickly. If this happens, then the entire batch of microgreens will need to be thrown away because they are no longer safe to consume.

Check plants’ stems and roots for discoloration if rotting is suspected. However, if microgreens’ roots and stems seem to be turning into somewhat thin, thread-like structures, then they have rotted.


Do the microgreens smell like a poorly ventilated basement? This can mean that mold has begun growing. Mold is an enemy to humans everywhere. If it can degrade a strong ceiling, imagine the harm it can cause to microgreen plants.

Mold development in microgreens can be caused by excess humidity plus inadequate aeration. To prevent mold growth, ensure optimal humidity, temperature, and ventilation for microgreen growing.

But could mold be mistaken for root hairs? People make this mistake all the time. They end up throwing away perfectly healthy microgreens because they think root hairs are mold.

Here’s how to distinguish mold from root hairs:

  • Mold affects parts of the batch while root hairs are even throughout the entire batch.
  • Mold appears towards the top while root hairs only appear at the bottom of the stem.
  • When water is poured on them, root hairs jump a bit while mold does not.

High Humidity Plus High Temperatures

Many novice microgreen growers think that a sauna effect, like that of a greenhouse, is the best way to grow microgreens. However, this is not true, and this could be the reason microgreens are smelling.

While ideal temperatures and humidity for growing different microgreens are somewhat particular to the specific species, 64 °F to 75 °F in temperature plus 40% to 60% relative humidity is favorable for most microgreens.

High humidity swells the plants and brings a musty odor to them. If it stays like that for a long time, fungal infections will occur that can worsen to root rot.


The cause of smelly microgreens could be that the growing medium used was made with chemicals of which the gardener wasn’t aware. Furthermore, it could be the plastic pots in which plants are growing that include harmful chemicals. Either way, the chemicals might be causing microgreens to smell.

The medium in which plants are grown is really important. Always buy seeds, substrates, and plastics from certified sellers. They may be slightly more expensive than the non-certified ones, but it’s worth the investment to be safe. Not to mention, buying from non-certified sellers is illegal and customers can be held liable by the law.

In Conclusion…

Microgreens are not like the mature plants grown in an open farm or greenhouse. They are delicate and susceptible to the slightest pathogens and harsh conditions. This may bring up undesirable smells in them.

Now that you understand what might be causing your microgreens to smell, you can use the above fixes to curb them and also learn to avoid them for good.

If you would like to get started growing microgreens or need a boost in your supplies, we highly recommend checking out our affiliate at True Leaf Market. They have microgreen seeds, supplies, starter kits, and anything else you can think of to make your production a success!

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Corey Leichty

Hi, I’m Corey and I love using gardening as a way to provide food for my family, learn life lessons alongside my wife, Andrea, and teach life lessons to my two sons. Do you have gardening questions? Not finding what you are looking for? Please feel free to Ask a Question (Click Here!) and I will get back with you as soon as I can!

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