How to Prevent the Most Common Microgreen Diseases from Occurring

This article will touch on the most common microgreen diseases (and some not-so-common).

But we don’t want this content to dramatize the possible health risks associated with microgreens (or any food), as problems are few and health risks are extremely low.

The common denominator of health risks posed by microgreens, like any food prepared or bought, is the due diligence of the grower, buyer, preparer, and consumer to be aware of possible problems, reduce the root cause of the issues, and use common sense.

Like all food that is alive before consumption, microgreens are also susceptible to pests and diseases.

If you are unwilling to accept any of these risks, please continue eating boxed macaroni & cheese.

swiss chard microgreens

The Most Common Microgreen Diseases & Pests

I had some problems with the title and headings in this article. Because what we are going to discuss aren’t diseases in my mind. They are living organisms. 

But I guess they’re thrown into the pigeonhole of disease in most people’s minds, so I’ll roll with this title.

Be aware that most of the discussion in this article will focus on “diseases” and not pests. 

We have published an article on microgreen pests, and you can view and listen to a podcast on pests by clicking this link.

home microgreens sells seeds

FREE Home Microgreens Grow course that teaches you the basics of growing microgreens in your home! There are 12 video lessons (over 120 minutes), downloads, and more written information and tips!

The most common pests and diseases of microgreens are:

  1. Fungal diseases: caused by a variety of fungi, including Alternaria brassicae, Botrytis, Cladosporium, Drechslera, Fusarium, Mycosphaerella, Penicillium, Phoma, and Stemphylium, and of course Pythium and Phytophthora, those that cause damping-off disease.
  2. Bacterial diseases: are caused by various bacteria, including Pseudomonas, Erwinia, Xanthomonas, Salmonella enterica, coliforms, and Listeria monocytogenes.
  3. Viral diseases: the most commonly found indoors is cucumber mosaic virus.
  4. Insect pests: caused by various insects, including aphids, fungus gnats, and whiteflies. These are discussed in this article.

Generally, to prevent and control these pests and diseases, it is essential to:

  • Use fresh grow media and certified seed.
  • Keep the growing area clean.
  • Sterilize trays after harvest.
  • Don’t reuse soil or other growing media.
  • Water microgreens only when needed – not on a schedule.
  • Inspect plants regularly for signs of pests or diseases.
  • Destroy infected plants.
  • Use traps and barriers to keep pests away.
  • Use organically approved chemicals according to the label instructions (last resort).
  • Much more discussion below.

Home Microgreens participates in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com. As an Amazon Associate, we earn from qualifying purchases. We may earn a small commission from the companies mentioned in this post at no additional cost to you. Not all links are connected to affiliate companies.

Fungal Diseases in Microgreens – Prevention

*Note: We will be writing an article about the damping-off disease soon and will link to that article here. Damping-off disease is caused by one or more fungal genera listed above. Therefore, it is more of a symptom of fungal problems than an actual fungus. 

Microgreens are a great way to get your daily dose of vegetables, but they’re growing living things and can also be susceptible to fungal diseases. 

You can do a few things to prevent or resolve these diseases.

Keep Microgreens Dry

The most crucial aspect to remember is to keep microgreens and the soil surface as dry as possible.

The best way to do this is to only bottom water microgreens. Watering microgreens over the top will wet the foliage, and the water will catch and hold any spores floating in the air.

Water on the leaves, stems, and the surface of the grow media gives tiny inconsequential fungus and bacterial spores to grow larger colonies up to the point where they may affect the plants or even you, the consumer.

led lights for microgreens

Give Microgreens Plenty of Direct Light

Make sure that your microgreens are getting enough light.

Exposure to direct LED lighting with Kelvin color temperatures above 5,000 can kill fungus and bacteria. At a minimum, microgreens should get at least twelve hours (we recommend 15 to 16 hours) of direct light per day.

If microgreens aren’t getting enough light, they will be more susceptible to fungal diseases.

use a fan to reduce mold chance

Air Circulation

It is also essential to place microgreens in a location with air movement. Even if this involves installing a small USB computer fan to move the air, these lightweight fans are easy to install on most microgreen racks or stands using zip ties.

Air circulation will improve drying conditions. Without moisture, fungi and bacteria can not reproduce.

Lower Seeding Density

Reducing seeding density is also essential.

Everyone expects microgreens to be densely seeded. Unfortunately, authors on many blogs and seed company websites suggest stupid seed densities.

If the tray isn’t wholly covered, they’re not happy. See this article, where I discuss how bad some seed density recommendations are.

If microgreens are too crowded, they will not get the air circulation they need, leading to fungal diseases.

We have a seed density calculator that gives conservative densities that have worked well for us. Click the link to see the Home Microgreens Seed Density Calculator.

plantign swiss chard microgreens

Try More Smaller Trays

Smaller trays are ideal for increasing air circulation around microgreens.

The distance to the middle of the tray is much longer in large trays than in smaller ones.

If you need more microgreens to harvest, plant more small trays instead of a larger 1020 tray.

The amount of seed and soil will remain the same, and the microgreens in the middle of the tray will be closer to the edge allowing better airflow.

Don’t Re-Use Soil

If you want to see fungus grow, re-use your soil or any other grow media. If I’ve ever had issues, it was because of used or poor soil. 

Don’t get me wrong, all soil and grow mats like hemp has fungal spores. It is 100% likely this is true. Even soils that are branded as sterile are not. But the number of spores is low.

Using it once doesn’t allow time for the fungi colonies to grow (especially if you keep the surface dry once they are under the lights). But give it another two weeks when you grow your second tray, and those fungal colonies will bloom. 

See the cover image of this article. Those microgreens are grown in reused soil. 

reusing microgreen soil by breaking up the root mass

I am separating plant matter from microgreen soil.

Lower Temperatures

Fungus likes to grow in warm and wet environments. So using heat mats or allowing the air temperature gets above 75 degrees F increases the chances that fungi will grow and colonize.

Sure, your microgreens might take longer to grow at lower temperatures, but fungus might not grow.

Good Agricultural Practices (GAP)

Another is good sanitary practices, such as washing your hands after handling plants and using clean tools and equipment. GAP includes many of the other factors we have mentioned above.

Sterilize and Dry Trays After Use

Start with clean and sterile trays.

You can rinse the trays removing any soil, then mist them with food-grade hydrogen peroxide, diluted bleach solution, and dry trays in sunlight. (it can break the plastic down, though).

If the tray is small enough, place the clean tray in the dishwasher and wash and dry it through the cycle.

Fungal Solutions 

If you notice that your microgreens are starting to get a fungal disease, you can try misting them with a fungicide. We suggest grapefruit seed extract, diluted white vinegar, or food-grade hydrogen peroxide (not the peroxide in the brown bottle – that has a stabilizer in it).

You can also try removing the infected areas and disposing of them. Use your fingers and pluck the inflected greens out of the tray.  

If the disease is severe, you may need to dump the tray, sterilize it, think about the possible cause, and start over.

Prevention is always the best cure, so make sure to take care of your microgreens, and they will take care of you!

Bacterial Diseases in Microgreens

Bacterial diseases can be a problem in microgreens. However, generally, you will not see microgreens distressed because of bacterial infections.

For the short time microgreens are grown, bacteria do not have enough time to affect the plant. However, this does not mean they will not affect you.

In fact, most people overreact to fungal issues with their microgreens. Most molds and fungi that grow on microgreens won’t harm you.

But bacteria are a different story, mainly because you can’t see the colonies.

The two most common bacteria are Salmonella and Listeria.

Salmonella (as well as E. coli) is often thought only to be found on animal products, but this does not mean that the bacteria can’t be transported to the surface of plants. Flies, no-see’ems, ants, and even our own hands and tools can spread these bacteria. 

Those bacteria may not thrive on plants, but they can survive and grow colonies if the conditions are favorable.

Do You Have a Pinterest Microgreen Board?

If not, why not start one! Use this pin as the first or add to your existing boards.

microgreen diseases

Bacterial Prevention 

There are a few different ways to prevent bacterial diseases in microgreens.

Don’t Use Compost

Never use unsterilized compost for microgreens. It is sure to cause Salmonella or E. coli outbreaks in your trays. Even if you don’t think animal by-products are in your compost, you forget rodents can and usually have visited your compost pile. 

Inspected Seed

Use seeds bought for resale for use as sprouts or microgreens.

Many seeds on the grocery store shelves are not tested for bacteria. The suspected use of these seeds is to keep the seed dry until cooked to a temperature that kills bacteria.

Those seeds are not for growing plants in environments conducive to bacterial growth.

Bean and alfalfa seeds from health stores are often grown as sprouts. However, these are not recommended to be used in that way.

Another often misused seed is black oil sunflower seeds meant for bird food. This is especially dangerous because those seeds are lower quality, stored in bulk at locations where rodents can roam, and sometimes the seeds are treated with chemicals.

It’s against the law to sell seeds meant for animal or pet consumption to be used for growing human food.

All of the Fungal Preventive Methods

The same methods discussed in the fungal section can be applied to bacteria too. 

Good Agricultural Practices (GAP)

It is good GAP to keep your trays clean, don’t reuse the soil or grow media, decrease seeding density, improve air circulation, lower the temperature, and keep the microgreens to help prevent bacterial problems.

Everything is covered with bacteria; there is no escaping it.

However, what can be done is to prevent the environmental conditions that allow bacteria to grow from occurring.

Like fungus, bacteria like moist warm conditions. Remove those conditions, and bacterial blooms will not occur.

Bacterial Solutions 

As with fungus issues, we suggest using grapefruit seed extract, diluted white vinegar, or food-grade hydrogen peroxide (not the peroxide in the brown bottle – that has a stabilizer in it) to kill bacterial growth.

Wash and Rinse Microgreens Before Use

This method is not a 100% surefire way to protect yourself, but it can’t hurt.

Viral Diseases in Microgreens

Many viral diseases can affect plants. These diseases can cause significant damage to crops.

But luckily for microgreen growers, viral diseases are not a problem. Again, microgreens are harvested before viral diseases can reproduce and be a problem.

fungus gnats

Microgreens and Insect Pests

Insect pests can be a significant problem for microgreens growers. The most common pests include aphids, fungus gnats, and whiteflies. 

These pests can cause damage to the plants by sucking sap from the leaves, damaging the plant tissue, and spreading diseases. 

Flies are particularly dangerous as they spread diseases and worms through the food they ingest. 

In addition, they can contaminate food with their feces, containing harmful bacteria such as E. coli and salmonella.

Microgreens need to be thoroughly washed before they’re served.

Several organic products can be used to control insect pests. However, read the labels carefully and follow the directions to avoid harming your plants.

Click the link for an article discussing the common organic controls for microgreen insect pests.

Final Word about Microgreen Diseases

Microgreens provide a very beneficial and healthy alternative to other vegetables. They are small, tender, and have a crunchy texture, perfect for salads or side dishes.

Microgreens can be enjoyed all year round and are a great way to get your daily dose of vitamins and minerals.

Don’t let this article be intimidating.

No one expects issues, and 99% of the time, there isn’t a fungal or bacterial issue. 

This doesn’t mean you shouldn’t be educated about possible problems and know what to do if they occur.

Prevention is the key.

Follow good agricultural practices because you are a farmer once you start that first tray of microgreens.

With the way the world is today, with food prices going up, the possibility of quarantines, and food shortages, you are better prepared to handle these events if you learn how to grow the essential foods in the home safely.

Growing your food is enjoyable and is a great life skill to master.  


  • Todd

    Todd is the founder of Home Microgreens & the Home Microgreens store. He also writes for several other websites, including MyViewFromTheWoods.com. Todd worked at a large farm market, garden & nursery center for 20 years. Somehow he snuck off to become a geologist and professor before coming back to his senses to write & lecture about microgreens and gardening. When not at the computer, he can be found in the garden, trout stream, or mountain trail with his new Springer Spaniel Caden.

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