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.

  • Mandy Shorey

    A bit new to the world of microgreens….I’ve been playing with different varieties to find what grows well and is tall enough to harvest easily (any suggestions would be appreciated). One problem I have experienced so far is root rot. The 2 varieties that are the worst are the Kohlrabi and the Mustard. Their roots get real slimy and brown. I’m using Biostrate Felt as my medium, water with a ph between 5.5-6.0 and has an air stone and pump. I started using 6-10 ml per gallon of hygrozyme to help with the problem but it’s not helping. I clean everything super well before using trays, I clean the reservoir weekly. I have played with different watering and I don’t think I am over watering.
    The other problem is my mustard microgreens. They start to fade in color 3-5 days under the lights and then a few more days in the leaves start to brown starting on the outside edges. I am using a T5 for light.
    I really appreciate some help about growing microgreens. It seems hard to find specific information or forums on the matter.

    • Root rot is very common and happens mainly because there is far too much moisture in your medium. My guess is that your felt may hold too much water and rot out the roots.

      For the mustard, you may need to add a light fertilizer if you’re growing in that felt medium (never done that myself). After 5 days the quick-growing mustard may be running out of nutrition from the seed.

      Hope that helps Mandy!

  • John Kochanowski

    My sunflower micros all of a sudden started dropping out after about day 8. They are BEAUTIFUL but the next day I come in and it looks like a trail of something went through and cut down a swath of trees! VERY frustrating. No rats so I know that isn’t a problem. I will say that this happens overnight. As a matter of fact, I went down to check things about an hour after the lights went out. Sure enough, the dropping had occurred! I’m wondering if watering just before the lights go out are causing some kind of reaction. I can’t imagine that is the case but damn… I’m not sure what else this could be.

    • How close are your lights to the surface of your plants? Are you watering enough? How deep is your soil?

      • John Kochanowski

        Kevin. There is about 6″ of clearance. I use a stack of trays turned upside down to help vary the clearance when needed/as they grow. I definitely keep an eye on the watering levels. However, the soil depth… I use 1″ trays and the soil is just under the top of the tray by about 1/4″ or so. I definitely need to consider adding soil all the way to the top I believe. Since I originally posted this I have had some beautiful harvests. This morning, on only day 5 I’ve noticed some “trails” again. I’m beginning to wonder if there is some type of snail or slug or other small pest working things over in the dark of night in the moist environment. Still very frustrating.

        One note: I’ve been composting my soil outside. I have to wonder if I am introducing a pest by not allowing the compost to fully “cook”. I have just purchased a long stemmed thermometer to gauge temp. I’ll update as soon as I figure this out. VERY frustrating!

        • That’s probably it. Too little soil for the sunflowers! I’ve done the same thing before.

          On the soil, You should probably use fresh soil instead of recycling compost until you can be fully sure it’s clear of any pests / etc. They’re very sensitive!

  • Gouri S Dange

    hi – i’m in india, and just started growing micro-greens. i grow them in inch-tall trays that come with the mushrooms that I buy, which I wash and dry. i find that the roots grow rather too prolifically inside the soil and touching the tray below. wondering if this reduces the size and succulent quality of the stalks. Any way I can prevent so much root formation? I tried to upload a picture of the roots after i harvested the micros. and the container in which i grow them – but am not able to upload.

    • It’s OK if they reach the bottom. 1 inch is a small depth. If your microgreens are still reaching about 3-4″ tall, that should be just fine. Roots can still provide nutrition to the plants if they are root bound!

  • John Kochanowski

    I just started trying to grow Arugula in soil and not having much luck. I cover them with paper towels and keep wet for a couple of days for germination which seems to be working pretty well. However, as they grow by day 5 or so they begin to dwindle. There seems to be a lot of dead growth mixed in with the beautiful growth… don’t know if it is due to watering from the top. I have fans blowing across my grow space constantly so air flow shouldn’t be an issue. Have to wonder if it is a combo of watering from the top that pushes them down in to the soil and a heavy sowing rate. Anyone else have issues with arugula? Seems like it should be an easy one to grow!

    • Hey John,

      I have not found the need to cover arugula in paper towels to germinate.

      You might find this article useful that I wrote:

      • John Kochanowski

        Thanks Kevin… I checked it out. Good stuff. Seems to me that maybe my arugula is just getting too much water from the top. I’ve scaled my planting rate to 0.7 oz per my 1″ 1020 tray. still looks like the watering from top is messing things up. I just purchased some “boot trays” that will allow me to water from the bottom. I’ll post some pics next round and see if you (or anyone else) can comment on progress/practices.

        I agree on your comments about washing. I’m on the fence whether to continue growing/selling any of these delicate micros that need to be washed.Growing in soil does have the drawback of needing a rinse which reduces the shelf life. Not good when trying to sell these guys. The other option I suppose is going hydroponic… something I’ve stayed away from so far.

    • John Kochanowski

      UPDATE: Resolved my arugula issues… they grow beautifully. I simply switched to covering the seeded tray with a Coroplast board. We leave them covered for about 4 days. when we see the tops of the yellow seedlings pushing the board up, we remove the corplast board and place an upside down tray for another day or two. After that, full light. We do uncover them and let them “rest” without light for at least 4 hours up to 8 hours. They seem to do best in my indoor single T5 environment for a total (seed to harvest) cycle of 12 days. I will experiment with changing to two T8’s and see if I can get the same results in a shorter timeframe. One additional note, I only water from the top one time, when the seedlings are about 1-inch tall. After that it is all bottom watering. I hope to have my site running soon where I can share the progress.

      • Great news, John. I’ve found Arugula is best harvested at around 12 days as well. I’m not sure about T8 v T5, from all of my research, T5 is just a more efficient light overall and should be run in place of a T8 or T12 no matter what. Keep me posted on your site.

      • Luis Eduardo Gómez De Aranda J

        Do you mean a single T5 light over them? What length are you using? How many trays do you cover with that single T5 light? Thanks!

        • I use the light I recommend here: – usually 4′ long and 4 tubes.

          • Luis Eduardo Gómez De Aranda J

            Yes, but for example, would you use one 4-foot T5 to light 5 of these trays? Considering they’re 10 inches wide, would a single 4-foot T5 be enough to light 5 of them?

            I’m asking about growing arugula by the way. Sunblaster seems to recommend using one tube for a width of 20 inches and a length of 4 feet (in case of 4 foot tubes, of course)

            Considering it’s in their interest to sell as many tubes as possible, I deem this information trustworthy.

            Do you think it would be enough? Can I cover 5 10×20 trays with a 4-foot T5 tube for growing arugula (not microgreen, mature plant)

          • Ah yes, you can. 5 trays placed width-wise along a rack would be ~50″, and 4′ is 48″ so it’d be perfect.

          • Luis Eduardo Gómez De Aranda J

            You have no idea how happy you’ve made me with this answer.

            I always see these T5 kits with many tubes stacked together closely (4 tube 216w kits mostly) and I was fearing that was the required light for growing. At 216 watts each it would not be economically feasible to grow arugula commercially in a vertical farm (with Spanish electricity prices at least).

            By the way, I’m going to check out Hortilux lights, specifically their T5 with UV light production. I will run some tests before committing to any manufacturer’s product, but the addition of UV light to the spectrum really makes sense to me – I could easily imagine getting tastier produce through the increased flavonoid production UV light will force my plants to.

          • Best of luck, Luis!

          • Luis Eduardo Gómez De Aranda J

            Thanks a lot man, this article was very helpful and inspirational!

  • najeeb khan

    Hi, we are trying arugula in hydroponic system, by using polyester as a supporting material for roots. we are facing several problem with arugula.
    In early stage after seeding all things going in right path, germination was perfect and plants grows perfectly looking healthy green, but after 10 to 12 days from seeding leaves are turns towards yellowing like all green part is bleached out, leaves are mold back, necrotic patches found on the leaves, tip burned. What the corrective action we need to done to rid of all these problems?

    • I would expect that after 12+ days, the arugula is starting to run out of seed nutrition and may need a light nutrient solution. Another potential issue could be the moisture level rotting out the roots as well. I hope that helps!

      • najeeb khan

        Thank you Kevin
        we already use slightly high nutrient solution, because we grow lettuce along with microgreens so we kept our EC in-between 2.1 to 2.3. In lettuce we also experienced the tip burning of the inner leaves specially with Lollo varieties.

        • Ah, that would be nutrient burn. Microgreens hardly need any nutrients at all, so try a much lighter solution 🙂

      • najeeb khan

        tip burning of lettuce leaves appears after 20 days from seeding.