• On The Grow, LLC

What is Damping-off? How it Affects Microgreens, and How to Prevent it?

Updated: Jul 2

Endive Microeens grown in Coco-coir

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Did you go to bed with beautiful trays of Microgreens, then wake up and check on them the following day and notice that you now have patches of die off on some crops? Then before you know it, half your tray is affected and you can no longer make it to harvest day....causing you to start the process over in hopes that this issue won’t happen again next time with your Microgreens... Well, we are very familiar with this, in fact it still happens to use every now and then with particular crops!

Damping Off on Broccoli Microgreens Tray
Damping Off on Broccoli Microgreens

What you may have a severe problem of is called, damping-off. You might not even be sure what it is. You may suffer from intense panic and just want to escape the issue altogether. Irrespective of your standing, there is a multitude of ways to avoid the disease from taking over. Here you will find the details you need to keep your Microgreens on a safe schedule.

First, What is damping-off?

You planted your Microgreens seeds with a ton of gentle care, looking over them like a hawk on the highway watching for a road meal. You dance while the seedlings sprout, then wail in pain as they fall quicker than they emerged. What happened to them?

Typically, the accuser is a parasitic fungus that has invaded the seeds. They have exciting names such as Pythium, Fusarium, and Rhizoctonia. If you really want to get scientific, Fusarium and Rhizoctonia are fungi, and Pythium is known as oomycetes. But who's going to count.

Sometimes the seeds don't germinate, sometimes they do and easily turn to the mulch soon after. It can be excruciating to lose a whole lot of seedlings and Microgreens in one go.

These fungal spores also live in the soil and can be spread by infected equipment, blown by the wind, or born by pests. Once there, it does not take much to ruin your trays of Microgreens or even your garden beds full of fragile young plants.

Symptoms of damping-off

Seeds or even patches of Microgreens die off that match the morning mush that you used to consume before college are a signal of contamination, generally results in a plant that never reaches the soil level. Wilting and blackening are symptoms, too. The leaves can look waterlogged and soggy. When the disease is suspected just in the roots, the plant's growth is inhibited, leading to withering and mortality. Affected stems may cause the plant to flop, breaking part way up the stem & turning brown, or it will even cause stringy stems that look like you have dehydrated them. You could also see a white, cobweb-like material in stricken places.

When you are considering your plants' symptoms, make sure you do not have any guilty parties to blame, like common mold, beetles and cutworms. The symptoms may look quite similar, but prevention and treatment are very distinct. So, keep a close eye.

Damping Off on Broccoli Microgreens Tray
Notice the stringy stems, this is a sign.

Biology of damping-off

It is almost difficult to prevent infected soil. These fungal pathogens are all over the world, and they do quite well where they are. The potting soil, in addition to shared water, provides an opportunity for them to move from seed to seed. The temperature of the indoor environment lets these party crashers move quickly.

That is not to suggest you are supposed to limit their fun by planting in the colder ground. This will slow down your Microgreens seedlings growth, giving even more time for fungi to grow and stand firm. A balance needs to be achieved with temperature, irrigation, lighting, and sanitation.

(Be sure to check out our blog on: Sanitizing and Cleaning Microgreens Trays)

Damping-off control and prevention

There is no remedy for it once your plants or Microgreens have begun to choke, and there are no fungicides sufficient to fight this battle, so it is all about control and prevention. You can avoid damping off by adopting a few basic techniques and tips.

Soil sterilization

There has been some concern about the sterilization of your growing medium. It is often an advised method to prevent fungal spores from killing your Microgreen seedlings, like baking your soil at 140 degrees for 30 minutes. Some schools of thought assume that these approaches destroy beneficial microbes that would otherwise hold pathogens in control.

No matter what you pick, it is probably better to use fresh soil for your seeds every time, especially since microgreens are grown in such dense seed quantities. If you are using your own outdoor dirt from your compost bin, it may be a good idea to give it a nice roasting first.

Tool sterilization

As your favorite Microgreens tools will take those disgusting spores straight into your freshly seeded trays or even onto your sprouted crops, make sure everything you use is safe before you sow or harvest. This can mean that you clean your tools yourself or use only new seeding and harvesting equipment for your Microgreens process. It never hurts to disinfect your equipment before and after each use, including your hose. In fact, we sterilize our reservoir every time before we refill it, wash & sterilize our trays after every use, sterilize or shelves after every rotation, sterilize our coco-coir bin after each use and we always clean and sterilize our harvesting equipment after/between every tray.

Sow smart

Keep it light and shallow when you plant your seeds, this is how you would typically want to plant… but with microgreens you sow in very dense quantities compared to traditional gardening. Which having many seeds induce precipitation, making evaporation quite hard. With that being said, always be sure not to over sow your tray! In case your curious, we provide a Free Downloaded PDF guide on the main page of our website that has our seeding density’s. Keep in mind, sowing too deep can slow down the production rate, allowing pathogens sufficient time to kill their hosts and limit airflow. Which means if you have a crop like Beet microgreens that prefer being under a layer of grow medium to germinate, don’t cover them with any more than 0.5inchs of soil/coco-coir.


We've heard you can try using a seedling heating pad to steam the soil to about 70 degrees for indoor planting. If your grow space is too cold, too hot, and even too humid… you could run into an issue with Damping off. If you feel like this is the cause, try making some adjustments and/or investing in a De-Humidifier.


Grow lights are advised to avoid damping off. Sufficient quantities of light can help Microgreens grow actively, providing rapid disease resistance. Typically, a window with low light will not be enough. Aim for at least 12 hours of light, maybe 16 hours.


Talking of warm, try using safe, lightly heated water to water your Microgreens. Cooler water can slow down the process of growth by potentially shocking them. Try to water from below with the bottom watering method rather than above, which makes things wet and offers fungi an edge. Try your best not to over water and provide enough time for evaporation, as you are likely tired of hearing by now that the humid, cooler night temperatures can offer fungal spores a benefit over your sweethearts. We water our crops twice a day, everyday, unless the grow medium is super saturated.

Damping Off on Sunflower Microgreens Tray
Look at the browning part way up the stems, this is also a sign.

What are microgreens?

Microgreens are edible seedlings developed to the first true leaf level. As you may of learned in our previous blog (click here), Microgreens have been famous with producers and buyers for a number of years. The need for microgreens has risen since they were established as a trend in kitchens after 2006.

Health-conscious customers and restaurant chefs are attracted to microgreens containing phytonutrients and plant metabolites. Added to sauces, sandwiches, desserts, and smoothies, served at home and in restaurants. Since they have such a limited shelf life, they usually are not grown on a large scale and exported for miles and miles like tomatoes, but distributed directly to local stores, giving smaller growers a chance.

Since microgreens are relatively easy to grow and have such a short growth time, they can be cultivated between crops in a greenhouse. They can also be produced all year round in greenhouses and colder climates. Profit margins are also reasonably large. An ounce of microgreens costs around 25 cents to harvest and sells for about 1 dollar per ounce in some places.

Growing microgreens is an easy and fun activity. If you are interested in growing your own microgreens, you must know all the basic techniques and pro tips to grow healthy, delicious, and disease-free microgreens.

Damping-off in microgreens

Pythium is among the most significant threats to microgreens. Damping-off can undoubtedly be a problem with microgreens. But that could be the product of a few cultural factors: too dense seed spacing in flats, zero air circulation & temperatures to name a couple.

Some types of microgreens are more vulnerable to disease and insect issues than others, such as Red Garnet Amaranth, Black Oil Sunflower, and some crops in the Brassica family.

Preventing damping-off in microgreens

The best practices that you may take to avoid disease are to pay careful attention to temperature, moisture, growing media selection, and spacing. Since there is such a short growth time for microgreens, the seedlings themselves are not treated with any chemical form. You may use some organic fungicides, however. Pay close attention to products label and apply accordingly. Personally, we prefer to mix our own mixture of h2o2 & Water at the ratio of: 2tbs 3% food grade hydrogen peroxide per 1liter of water. Which in some cases we'll preemptively mist our seeds with this mixture during the germination stage to be extra cautious.

The other disease element worth remembering is the seed itself. In fact, the very first phase of prevention is to get good quality microgreen seeds. Seeds can be susceptible to pathogens, so it is preferable to gain a healthy seed. Some growers even like to sterilize their seeds before sowing.

Like we said before, sowing too many seeds can also be an issue and increase your chances of running into Damping Off, just like improper sanitation…

With all this in mind, remember to always be cautious and make the best choices for your seedlings and young microgreens. If you start to notice a issue, make minor adjustments until you solve it… and never get discouraged! Crop fails are how you learn and become an expert.

On The Grow farms Various Microgreens in 5x5 Bootstap Farmer Trays

Want to learn EVERYTHING we learned from all our years of growing and experimenting with microgreens? Or maybe even learn some new recipes to use your Microgreens in?? Then check out our eBooks below!

Becoming a Microgreen Master eBook by On The Grow:

(Click here for Kindle) or (Click here for other devices)

Recipes for The Everyday Microgreen Lover, Vol. 1 eBook by On The Grow:

(Click here for Kindle) or (Click here for other devices)

Curious about other supplies we use?

Check out our Amazon Affiliate Store Front by clicking (here)

Or if your looking for a trusted Microgreens Seed supplier,

Check out this company that we love by clicking (here)

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Written by: On The Grow, LLC

Published: December 14, 2020

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