If Your Microgreens Smell, This Might Be Why

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Are your microgreens, smelling foul? This bad odor is the result of molding, rotting microgreens! They are being damaged due to overwatering and other environmental conditions.

Why Do My Microgreens Smell? Foul-smelling microgreens have generally been overwatered, and the plants have developed mold or stem rot. There are other factors, which contribute to smelling microgreens, which include overcrowding, high or low temperatures, insufficient airflow, chemicals, or high humidity.

My neighbor had a greenhouse in his yard, and he had a wonderful irrigation system of sprinklers, which sprayed a very fine mist onto his plants. I learned this was one way to ensure that his greens would not become saturated with water. Airflow is also equally important! The circulation of air regulates the temperature and humidity. What he applied to his greenhouse, goes for microgreens as well. Learn more tips and tricks to grow healthy microgreens right here. 

Reasons for Foul Smelling Microgreens

There are six main factors, which contribute to smelly, moldy, rotting microgreens:

OverwateringOverwatering is the main reason for mold and stem rot. This is due to the excess moisture found on the leaves and against the stems of the microgreens.

Mold, which thrives in these conditions, disperse their spores all over, therefore spreading the spores over unaffected areas. Water that has accumulated against the fragile stems causes stem rot.
OvercrowdingMicrogreens are often planted in such a way that they are overcrowded, but this overcrowding can cause water to be trapped around their spindly stems, and stem rot can occur. Overcrowding can also cause the leave to become yellow, due to not enough light or sunlight.
High humidityKeeping the humidity low will prevent mold and stem rot. High humidity is caused in heated conditions and where there is too much moisture in the air. This is not good for microgreens, because although they need a fair amount of liquid, excessive amounts of water vapor will cause the plant to develop mold or stem rot.
Irregular temperatureToo high or too low temperatures can stimulate the growth of mold on the microgreens. Greenhouses can become very hot if they do not have proper ventilation. If temperatures are too hot, the humidity may become very high, causing mold and stem rot.

On the other hand, if the temperature is too cold, water will not evaporate and will accumulate around the roots of the plants.

Low temperatures also encourage mold spore activity as spores are usually dispersed in cooler conditions.
ChemicalsChemicals can contribute to foul-smelling microgreens. Plastic flats, which are the trays where in which the plants grow, may be made of poisonous plastics.

Plants often need to be sprayed by chemicals for pests or other reasons. Too much of these chemicals may destroy the plants.

Chemicals in the soil may also harm the plants.
Unsterile equipment & soilUnsterile flats can cause mold. These should be sterilized before planting a new batch of microgreens.

Soil may become contaminated, so it’s also important to renew the soil when sowing new seeds. This will prevent plant loss.

Prevention of Mold or Stem Rot in Microgreens

Ways to prevent foul-smelling microgreens:

  • Install an irrigation system: Use an effective irrigation system. An overhead irrigation system that sprays a light, a fine mist of water over the growing plants is very effective. This will ensure that the plants and soil will not become too saturated with water, therefore preventing mold and stem rot.
  • Spread plants out: Overcrowding of microgreens needs to be checked! Molding microgreens must be removed as the mold will spread to other unaffected plants.
  • Use a dehumidifier: Install a dehumidifier in your greenhouse. This will decrease the chance of the greenhouse becoming too humid. Set your humidifier on 50 to 60%.
  •  Create airflow: Increase the airflow in your greenhouse, using fans to circulate the air. Good air circulation will prevent excess water and humid air from damaging the microgreens.
  • Regulate the temperature: Microgreens should grow in temperatures between 60 and 80 degrees Fahrenheit. In cold climates, it is advisable to install some type of heater in your greenhouse. On the other hand, a cooling device will be needed in very hot climates.
  • Avoid chemicals: Avoid using too much chemical on your microgreens. New clean soil should be used when sowing new seeds and avoid soils which have a lot of chemicals in them.
  • Sterilize equipment: Always use sterile equipment when planting new seeds. Sterilize your unused flats, by inserting them into a sink of water and bleach or food-grade hydrogen peroxide.

All My Microgreen Plants are Infected with Mold!

Help! All my microgreens are wilting, smelling, and covered in mold! What must I do?

If your microgreens are yellowed and when examined up-close display a white, web-like film of mold covering the plants, here is what you need to do:

Fill a spray bottle with:

  • 1 ½ liter of water
  • 50 ml of white vinegar
  • 50 ml of food-grade hydrogen peroxide.  

Spray the plants evenly, not spraying too much. A coating that is sprayed too heavily can cause microgreens to burn. 

A note about mold: Remember that some seedlings develop fuzz at the base of their roots. This may look like mold, but it is not mold, but part of the germination process!

RELATED: Why Microgreens Mold and How to Prevent It

How to Grow Microgreens?

If you’re wondering how to give your microgreens the best start, the directions are simple!


  1. Select the type of seeds you wish to grow (seed selection from Amazon). You’ll find a great variety of microgreens, used to flavor dishes, as well as to enhance nutrition and health.
  2. Purchase flats or trays that have holes at the bottom for drainage. These trays must have another tray underneath to catch excess water.  
  3. Buy a good potting mix.
  4. Pour your potting soil into the flats. They should be filled 1 inch to the top of the flats.  
  5. Not all seeds should be soaked, but in some cases, they should be. Soak the seeds in a bucket of water for about 6 to 12 hours. If the seeds are very small, place them in a material bag before placing them into the water. This improves the germination rate. 
  6. Sprinkle the seeds onto the soil and pour a thin layer of soil over them. Place another tray over the seeds and leave for three (3) days.
  7. Water your microgreens twice a day. Microgreens need a lot of water but remember not to overwater! Regularly remove any excess water in the lower trays.
  8. Once they have started to grow, they may look yellow, but this is because they have not been exposed to sunlight. After a few days, place them under a grow light or where they can get indirect sunlight. Avoid direct sunlight, as this may burn your plants.
  9. Microgreens can be picked once they grow their second set of leaves known as true-leaves. Some growers allow their plants to grow an additional week to produce baby greens. The average time for microgreens to grow is between 7 and 12 days.

Ways to Serve Microgreens

It’s truly rewarding to grow healthy microgreens and once you have started, you don’t want to stop. You can serve your microgreens in so many ways. Let us share some of our favorites:

Salads: Sunflower shoots are delicious in tossed salads. Raw microgreens do well in salads. Due to not being cooked, they are fresh and crisp with delicate flavors.

Sandwiches and Wraps: Radish greens give a spicy flavor to tortillas and wraps.  

Stir-Fries: Radish sprouts do well in stir-fries but must be tossed in at the last minute.

Smoothies: Add wheatgrass or radish greens to a citrus-based smoothie. Wheatgrass is used for those who want an optional health drink.

Baking: Why not put sunflower sprouts in your quiche! They will add a little flavor, which spinach cannot achieve. A little handful of radish sprouts in your summer berry pie, will add a hint of spice and offset the sweetness of the berries.

RELATED: 35 Tasty Ways to Use Microgreens

Know the causes and be successful

Growing microgreens is in general easy, but you may encounter problems that make your crops go bad. Knowing in advance what causes microgreens to smell and making them bad is your best tool for success. Always follow the steps on how to grow microgreens and use proper equipment. Get the environment where you want to grow prepared, don’t overwater (which as mentioned is one of the most common reasons for foul-smelling microgreens) and keep distance between the seeds. These are some of the key factors for success!

Microgreens Corner
Microgreens Corner
We are Janette & Jesper, and we love microgreens.


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