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!

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.


Kevin is the creator of Epic Gardening, a community dedicated to teaching urban gardening, hydroponics, and aquaponics. He enjoys skateboarding, piano, guitar, business, and experimenting with all kinds of gardening techniques!

  • Darko

    Mold, mold and mold again. I’m becoming frustrated by this problem. I sterilize seeds before use by hydrogen peroxide, germination is always excellent but than on day 3 or 4 mold occur.
    pH is 6 and I’m using polypropylene mat. I’m not using ventilators is this a problem?

    Thank you for your answer, Darko

    • Hey Darko,

      Thanks for the comment. Mold is something I had HUGE problems with for a while. Make sure that these things are in order:

      1. You’re not planting the seeds TOO densely together.
      2. You’re not over soaking your polypropylene mat (these are very absorbent)
      3. You don’t have high humidity + high temperature combination

      If you still have problems, you may need to try germinating in a dark room but leaving them uncovered and using a fan to get airflow. Mold HATES airflow. You may also want to experiment with a different growing media, though you can make those mats work as long as you don’t over soak them and mist lightly but not too much. The sooner you get the tops off of your trays, the better…even if you have to expose to light earlier than you might normally want to.

      Let me know how it goes!


  • ashley

    My micros were doing so well for about a few months and are now growing clumpy together and look weak, I have tried adding a fan to the room I grow in and I’m starting to think it’s the lights I have them under, I’m not sure though because they were growing fine in the same room under the same lights for quite a while. Now I’m wondering if I took the lids off too soon or too late? I have been pretty consistent with everything over the last couple months and I’m just feeling frustrated now. It’s like they are growing completely different each week for the past three weeks. Any advice?

    • Hey Ashley,

      Sorry to hear that 🙁

      It could be a few things:

      1. The lights could be evaporating the soil too quickly and leaving your fragile micros wilted.

      2. You might have accidentally planted the seeds too close together. Sometimes they can stick together and grow in little bunches.

      3. It could be that you took the lids off too late, sometimes that causes the micros to stretch too far in search of light, and then they’re too weak to support themselves when you do take the lids off.

      Some general advice: I’d take some detailed notes on planting time, amount of water, the type of seed, and the amount of seed that you planted, as well as the amount of time you leave it covered up. If you notice any differences in your notes that correlate to worse plants, you know what to fix!

  • Milen

    Dear Sirs,
    I have been struggling with fungus for quite a while now… I managed to save my buckwheat micrigreens but it keeps getting the sunflower, so I decided to follow your advice and use grapefruit extract although it is a bit on the pricey side… can you just tell me a bit more on how to use it – in what proportions do I dilute it, do I spray only the places where I see the fungus appearing? Do you think if I spray locally only the infected places I could save the rest of the crop or I should discard the tray once it gets infected? Thank you

    • I would use a few drops only – it’s very strong. I would give a light spray to everything if you have mold, but the best thing to do is scrap it, spray everything down with food grade H2O2, then wait a day and start over. It sucks, but it’s one of the only ways to kill all the mold!

  • Andrew K

    How the heck do you get the seeds off micro cilantro when processing!?

    • epicgardening

      Hah, great question! One of the more annoying ones for sure…

      I try to brush them all off BEFORE I cut any of the greens down, that way I can use the strength of the roots to apply a lot of pressure to the top of the plant.