Common Microgreen Problems


While growing microgreens is relatively simple when compared to a lot of hydroponic plants, you can still run into a lot of different problems.  In the microgreens business that I have recently started, I’ve found that it’s been a challenge to control for all of the different things that can go wrong when growing restaurant-ready microgreens.

Here are all of the microgreen problems I have run into, along with how to solve them!

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Mold or Fungus

This is one of the biggest problems I’ve run into due to my 70 degree + summer temperature and high humidity the past few months.  There is a BIG difference between mold and root hairs, which are concentrated around the main root of the seed and are very beneficial for a plant at the beginning of its life.

You will find that white mold looks like a spiderweb crawling across the surface of the growing media.  It starts out in one area in a small, wispy ball and then expands quickly over the growing media.  If you don’t take care of it, pretty soon it will climb up the stems of your plants and your entire crop is ruined.

The Solution

  • Make sure your trays are CLEAN before you plant
  • Decrease humidity by increasing air circulation (hard in the blackout period but you can partially uncover the trays)
  • Decrease the seed density of your future trays, especially for mucilaginous seeds
  • Try using Grapefruit Seed Extract mixed with water as an organic solution

Slow Germination

Most microgreen seeds germinate within 2-4 days, but some take a bit longer.  If you’re seeing much longer germination times, something is wrong.

The Solution:

  • Increase moisture in the tray by spraying more / more often
  • Do a germination test with some of your seed in a wet paper towel

Yellowish Microgreens

This isn’t a very common problem, but it can happen sometime.  Before you take the blackout dome off of your microgreen trays, all of your seedlings will be yellow.  This is because they have not been able to take in light and start the process of photosynthesis.

The Solution:

  • Take the blackout dome off of the trays earlier
  • Place trays near a stronger light source

Clumpy Microgreens

When you’re spreading your seed out in trays, it can be difficult to get an even spread.  Sometimes if you plant seeds too densely they will clump together, especially if they’re mucilaginous.  When they sprout, a few of the seedlings will “push” the rest of them up into the air, suspending the roots and possibly bringing dirt along with them.  This makes it very hard to harvest.

The Solution:

  • Decrease total seed volume planted per tray
  • Spread seeds more evenly throughout the tray

Weak Looking Microgreens

This is an all encompassing condition that covers the rest of the problems that you’ll have.  It’s hard to troubleshoot exactly why a particular microgreen crop is doing poorly if you’ve already made sure you don’t have any of the conditions above.

In my case, a lot of the weakness I saw in my crops was due to a lack of moisture control – either too dry or too wet.  In some cases I didn’t properly prepare the seed before planting it, and in others I took the blackout dome off too earlier or too late.

The Solution:

  • Be very sure to read the seed packets very carefully to see what you need to do for each type of microgreen
  • Stick to a normal watering and misting schedule
  • Different crops need the blackout dome taken off at different times – be sure to be crop-specific
  • Some crops need the blackout dome flipped upside down on top of them to make them “struggle” to thrive

That should cover most of the problems you’ll have with microgreens.  I’ll be talking more about them in the future, but in the meantime you can take a look at the main microgreens page to see what aspects of growing microgreens I’ve already covered.

I’m the founder of Epic Gardening, a website dedicated to teaching 10,000,000 people how to grow plants. I enjoy skateboarding, piano, guitar, business, and experimenting with all kinds of gardening techniques!

Learn how to solve common microgreen problems in this part of the Epic Gardening Microgreens Growing Guide!
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65 thoughts on “Common Microgreen Problems

  1. Hi Kevin

    I am growing microgreens and I have noticed some very pale not quite brown shading on my 2 inch tall sunflower microgreens. Is this normal, they are strong, taste great and other than that look great too, I wondered if they needed a liquid seaweed spray?

    • If you grow them for a while, or in completely nutrient-devoid media, you can get some pale-ness to them. Could also be a sun issue. If they taste good, I wouldn’t stress too much!

  2. I’m not watering my microgreens from the top only misting them. Yet there are patches where the microgreens fall over and make the whole tray look bad. Am I not putting enough seed in that

    • I would bottom-water your microgreen trays and make sure they’re nice and moist. Typically sections falling over are either too dry, or suffering from dampening off disease.

  3. I was experiencing mold issues but I cleared it up using less water and removing dark out lid at night for fresh air but now I believe they have gotten some light because the have a tint of green on them is this bad?

    • Yeah, good call. It’s not bad for them to have green on them, just means they will grow a bit faster and the stems will be less long as they won’t have spent as much time stretching out.

  4. Hello! So glad I found your site. You have such great information about EVERYTHING! I am going to start growing microgreens in my basement and was wondering what temperature they need to be grown in. Although heated, our basement is typically around 54ish degrees overnight and maybe around 60 degrees during the day. Is this too cold (it is for me!). Should I use a tent of some sort? I’ve started oodles of vegetable seeds in the basement but I also used a warming mat. Those things aren’t cheap though so I’m not sure I want to buy a bunch of them. Thanks!

    • 60°F is fine for micros. Just make sure they have enough light! I’d definitely use a seedling heat mat though to speed up germination and keep them nice and warm. Most seeds want to be a bit warmer for germinating 🙂

  5. Hello – I’m growing microgreens for a restaurant in soil and have been battling a serious aphid issue. I’ve taken out all the trays, bleached, and used new soil, but I must be missing some aphids or bringing them in from other sites as the issue arises eventually. Do you have any tips on pest prevention or control for microgreens? I spray Gnatrol and Mycotrol once a week before I bring the trays to the client, but I can’t spray anything too intense at the client’s site as it’s exposed to the public. Anything help is much appreciated!

    • Hm, I’ve never had a pest issue with microgreens due to growing in 10×20 trays (easy to control environment). You should do a FULL scan of your growing space and if possible grow in a different area with 100% clean and sterilized equipment until you get to the root of the aphid issue in your growing space.

  6. Hi my problem hier in de caribbean is gnats in soil or buks. Sorry for my inglish.
    I try to not watter to much but still i have the problem.
    Indoors in a papel towel they dont grow as in soil more true leaves. The smell indoors is not so nice
    Dos someone have a organic solution for this. Something that works.

  7. My 1st batch of microgreens mesclun mix is now 13 days old. Starting to show 1st true leaves. I’m curious about the dark dots showing up on the cotyledon leaves. Could these be pigments from the red leaf lettuce or mold? The don’t rub offline mold and don’t taste weird. Yes I ate one to find out. Any advice?

  8. Hi, I soaked and rinsed my peas, plated but within 2-3 days they become slimy and smell sour!! They are so germinating but the smell is bad! I use to use snow pea never had this problem switched to a spealisit microgreens pea and now this??? ( snow pea is too expensive) any idea what’s going wrong?

  9. I’ve been having the hardest time with my micros. My first two crops were amazing and grew perfectly. Now the last three batches I’ve done they have germinated just fine. But then out of no where they start to die off. I planted some lemon basil in a 5×5 tray. And it’s only growing In some spots. The rest have died off. Idk what I’m doing wrong!? They have been growing in patches and idk how to solve this problem. I don’t know if they are getting to cold over night or what’s happening. It’s very frustrating though. Lemon basil is like my best seller and I can’t grow it if my life depended on it lately. It’s not just my basil tho. My spicy salad mix has been doing it to. My soil is coconut coir, earthworm castings and azomite. I need help! I grow them for my restaurant to and lately I haven’t had any micros to garnish my plates with.

    • Lemon basil is a tricky one, as are all types of basil because they’re a mucilaginous seed (create a gel around themselves), which causes them to stick together and pull themselves out of the soil. Make sure you don’t plant too densely. They also take quite a while to germinate relative to other micros. Are you recycling your soil at all? I would take very careful note of the moisture levels in your soil and if you are changing ANYTHING compared to the trays that are doing well. Sorry – all I can offer are some general suggestions without being there!

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