Troubleshooting the Top 10 Microgreen Growing Problems

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You’ve started growing your own microgreens but maybe things aren’t going so smoothly. Your microgreens just don’t look like all those pretty pictures you see online.

No…..

Yours seem to be plagued with problems.

Yeah. Been there. Done that!

Microgreens are a great way to add fresh greens and herbs to your diet, but sometimes they can be difficult for people just starting out.

I understand.

So, I’ve collected the Top 10 Problems when growing microgreens. Read up on which problem/problems you’re having and see if these tips help.

Table of Contents

Microgreens Seeds Planted too Densely

If you plant too many seeds, especially seeds like Chia that are mucilaginous, it could cause clumping, reduce air circulation between the plants and cause mold to begin growing.

Overwatering

  • Overwatering is the most common reason microgreens develop mold.

  • Water your microgreens every one to two days or when the growing pad feels dry or when the pad begins to feel dry.

  • If water “pools” on top of your soil, you’ve overwatered.

  • Empty the drainage tray. If you don’t, this will greatly increase the humidity around your microgreens increasing your chances of mold.

  • Let the leaves dry in between watering.

  • Use growing trays with drainage holes.

  • After watering, place your trays in a sunny location to help the leaves dry.

 

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Inadequate Light

You need to give your microgreens light every day. If your main source of light is natural, be sure they get a minimum of 6 hours. When using artificial lighting, they’ll need light for twelve hours using a 20-watt bulb.

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Humidity Dome

Leaving your humidity dome on your trays too long can cause moisture to form. The humidity dome should only be used while the seeds germinate. Once you see your seedlings, take the dome off or too much moisture may form causing mold to grow.

How do you remove the mold?

If you see mold on your microgreens, you should immediately remove all the mold you can see with a soft cloth. To clean the microgreens, gently take a cloth and wipe it across all the microgreens.

You can also remove sections that have mold if it hasn’t spread to the entire tray or spray using hydrogen peroxide to kill the mold.

It’s possible to remove some mold, but “prevention is worth a pound of cure.” In other words, start well.

  • Remove any leftover soil from previous crops.

  • Spray your trays and wash them with soapy water.

  • Disinfect or sanitize your growing trays before replanting by spraying the trays with hydrogen peroxide and letting them sit for at least 20 minutes.  Use 1 teaspoon of 3% h per gallon of water.

  • Use quality soil.

Growing Microgreens

Problem #2 – Microgreens Falling Over

There are multiple reasons your microgreens are falling over.

Not Enough Light

One reason your microgreens are “leggy” and keep falling over is that they might not be getting enough light. Remember, you need to give your microgreens light every day and if your main source of light is natural, they need to get a minimum of 6 hours. When using artificial lighting, they’ll need light for twelve hours using a 20-watt bulb.

Blackout Time

And once again, you’ve got to get that “blackout time” right. If they stay in blackout after they’ve germinated, they’ll continue to grow, but without sunlight. This creates weak, spindly microgreens that can’t stand up.

Incorrect Watering

You may be over or underwatering. If you’re underwatering, the roots won’t have enough water and start to dry out leading to wilting.
If you’re overwatering, it can lead to seeds damping off, causing the roots to rot. This could cause your microgreens to fall over.

Incorrect Harvest Time

You could be waiting too long to harvest your microgreens. Waiting too long to harvest leads to “leggy” plants, causing them to fall over. Once the first set of true leaves has emerged, harvest your microgreens.

Overhead Watering

One more cause of microgreens falling over is overhead watering. Microgreens are delicate little plants. If you choose overhead watering, it’s best to use a mister. Your typical watering can (even smaller houseplant watering cans) won’t do unless they have a small nozzle. A spray bottle as simple as this one will do:

Or choose a watering can with a small tip like this one:

How to Grow Microgreens

Problem #3 – Slow Germination

So, you’ve planted your microgreens seeds and waited for them to sprout. You’ve watered them, you’ve fertilized them, and you’re excited to see them grow! But it seems to be taking too long. What gives?

Different Growth Times


Microgreens take a long time to grow. Most greens can be sown within 2 to 3 days and ready to harvest within 8 to 21 days. 
There are fast-growing microgreens and slow-growing microgreens and you have to keep this in mind when growing them. The slower-growing varieties need up to 25 days before they are ready to harvest, while the faster-growing types only need eight to 15 days. Each type of microgreen has its own crop cycle.


Larger seeds, such as sunflower, peas, beetroot, wheat, and mung beans take longer to germinate. To speed them up a little bit, soak the seeds in warm water overnight or even for just a few hours. Be sure to drain and rinse the seeds before sowing.

Sufficient Water

Your seeds need the correct amount of water to begin the hydrolytic process. The water softens the seeds and prepares the stored food in the seed ready to be used. Without enough water, the seeds cannot begin this process.

But of course…

Too much water causes poor germination and could compact your growing medium. If you compact your growing medium, your plants may not get enough oxygen. So once again, pay attention to the instructions your seeds came with and carefully follow them.

Correct Blackout Period

As important as the right amount of water is to germination, having a blackout period is equally important.

After you have prepared the growing medium, watered, and sown the seeds, it’s time to cover your growing trays so you can trick the seeds into thinking they are under the ground. Seeds require this period of darkness before they can germinate.

But don’t put your microgreens trays in the pantry or basement and forget them. This germination stage is crucial and they must be kept moist.

Correct Temperature

Another very important aspect of getting your microgreens to germinate properly is making sure you have the temperature correct. Are they in a cold basement? Are they sitting next to your radiator during the wintertime? A good rule of thumb is to keep the temperature around 70 degrees Fahrenheit – not going below 60 degrees or above 72.

Once the seeds have germinated and it’s time to take them out from the dark, they need light to grow healthy.  If you can’t provide natural sunlight or enough light in the space where you grow, there are alternatives such as using artificial growing lights.

If you live where you have issues with controlling the temperature for your microgreens, you might need to consider getting a seedling heat mat. Check out “The Best Seedling Heat Mats of 2021” for complete reviews and affordable prices.

Sprouts vs Microgreens

Problem #4 – Microgreens Have Uneven Growth

Yes, we all want those perfect, pretty trays of microgreens. Well, at least I do anyway. 

Two of the most common reasons trays of microgreens end up growing all wonky, is;

Uneven Light


It all depends on your setup, but most likely, you’ll have to rotate your growing trays if you depend on natural light. Since they’ll need roughly 6 hours of light, chances are you might have to move the trays to different rooms.


If you don’t rotate or move the trays, you’ll have microgreens that are different sizes and that lean toward the sunlight.
If this is a problem or seems like a pain, you might want to try plant lights like these:

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Too many Seeds


It might not seem like sowing seeds too densely would cause them to grow unevenly, but it does. Some seeds get “chocked” out by others and their growth is stunted. 


You’ll also get uneven growth due to the fact that all seeds don’t germinate at the same speed. Yes, even if they are all the same type.

Growing Microgreens

Problem #5 – Clumped Microgreens

Yeah, you want microgreens that look like that! I feel you! When I first started out growing Microgreens, mine didn’t look like the picture you see above. 

Nope…

Some of mine would be a weird clump of “growth.” As the microgreens grew, they seemed to push some of the others up and I would have a strange-looking mass instead of nice pretty trays of microgreens.

Live and learn.

This is caused by planting the seeds too densely. They’re sort of growing right on top of each other or fighting for space so to speak. This is an easy fix. Simply sow fewer seeds per tray. Concentrate on sowing the seeds more evenly.

Here are a couple of tricks to sow seeds evenly:

  • Put your microgreen seeds in a salt shaker and shake the seeds out onto the tray.

  • Mix your microgreen seeds with sand. Pour a handful of dry sand in a cup, add the seeds and mix. Next, sprinkle the sand/seed mixture over your growing tray.

  • Make your own “seed tape.” Mist squares of toilet paper. Sprinkle seeds on the toilet paper and lay the toilet paper seed-side down in the tray.

Problem #6 – Microgreens Invaded by Pests

Unfortunately, we’re not the only ones that love microgreens. Little irritating creatures love them too. If you have noticed some tiny bugs swooping around your microgreens, they’re probably fruit flies, aphids, whiteflies, or thrips.

Fortunately, having pests when you grow microgreens inside isn’t as big an issue as when you grow them in greenhouses.

The best way to approach pests in your indoor microgreens is by preventing them. To do this, always use a growing medium from a reputable nursery or garden store. Do not use dirt you brought in from outdoors. You could be bringing the pests in with the dirt.

aphids
white fly

How Do I Know if I Have Pests in my Microgreens?

Knowing what to look for when it comes to pests is important because it will help you to take care of them. 

Aphids feed on soft stems and leaves. They pierce the stems and suck the nutrient-rich sap from the plant, leaving behind curled or yellowed leaves.

Whiteflies feed on the sap that flows from growing leaves. The adult whitefly sucks the sap then deposits the sticky residue of its meal on the undersides of the leaves. In doing so it prevents the leaves from developing and eventually kills the plant. Plants become weak and susceptible to disease. Pests, like aphids and whiteflies, secrete honeydew, so leaves may be sticky or covered with a black sooty mold.

The first thing to do to determine you have pests, is to look at the leaves. If they are turning yellow and wilting, it could be a problem. If you see any holes on the underside of the leaves, this could mean that a pest has invaded. Look at the stems. If they are blackening or rotting, you have a problem.

yellowing microgreens

Problem #7 – Yellowing Microgreens 

First things first. Before you do anything, read the seed packets that came with your microgreens. If you buy quality seeds from a reputable source, the packets will have detailed growing instructions including how much light, water etc. If your seed packets don’t have growing information, go to the company’s website and look up instructions there.

All seedlings will be yellow when they first come out of their “blackout time.” This is because photosynthesis hasn’t had a chance to take place. Once the seedlings get some light, they’ll start to “green up.”

Different seeds require different blackout times. So, what’s a “blackout” time or period? This is the time period immediately after planting. Microgreen seeds need anywhere from two to eight days of darkness.

Why?

This gives them a chance to germinate. Basically, it simulates covering the seeds with dirt as you would do in an outdoor garden. When growing microgreens, you don’t cover the seeds with soil and you sow the seeds compactly. If you covered the plants with dirt, as they grew, they wouldn’t knock the dirt off and when harvest time rolls around, you would end up with a dirty crop.

Because the blackout period is crucial for germination, you’ll need to improvise. We usually use trays that come with a blackout dome, simply because it is convenient. If your trays didn’t come with a blackout dome you can simply turn an empty grow tray upside down over the new crop. If the tray has drainage holes in it, cover the holes with cardboard or old towels so no light creeps in.

Unfortunately, the causes of microgreens turning yellow are many…and confusing. It could be too much light. Not enough light. Too much water. Not enough water. The blackout period is too long. The blackout period was too short.

You get the idea. 

This takes trial and error. As you start growing microgreens, start with one or two types. See what works best with that particular microgreen before moving on to your next choice.

 


Problem #8 – Leggy, Weak, and Pale Microgreens

When you grow microgreens, you want them to look like all the pretty, healthy, vibrant microgreens you see online. 

Right?

So, it’s very disappointing when yours turn out looking sickly. The causes of leggy, weak, and pale microgreens are much the same as the “yellow microgreens” problem.

The most common causes of “leggy” microgreens are:

  • Your microgreens might have had too long a blackout period if they are stretching out and “leggy.”

  • Some microgreens are supposed to look yellow (like popcorn shoots, and yellow beets).

  • They might not be getting enough light or they need brighter light.

  • Their roots may be under attack from mold or bugs.

  • The water pH may be off. The water needs to be neutral for proper nutrient uptake through their root system.

  • Seeds sown too densely may be blocking light.

Troubleshoot the problem with “leggy” microgreens by checking for each of these problems eliminating each issue until you find the culprit.

How to Grow Microgreens

Problem #9 – Stinky Microgreens 

It is normal for seeds to have a distinct scent. If your microgreens stink, they have most likely been overwatered, and have developed mold or stem rot resulting. Mold and stem rot can also come from planting your seeds too densely and overcrowding your plant. Another culprit is very high or very low temperatures, inadequate airflow, or high humidity.

Any of these issues can result in microorganisms that have taken over, giving your microgreens a bad smell. If you’re not sure, give them more time to grow. If the smell is still lingering when your plants are 1” to 3” go ahead and toss them.

Problem #10 – Dirty Microgreens

Seeds grow traditionally in nature or in the garden if they are covered with a layer of soil. Being covered by a layer of the soil gives the seeds a chance to germinate. Seeds need to have darkness created by soil to do this. But, it’s a little different for microgreens.

The best practice for germinating microgreens is to simply sow the seeds on top of the soil, then cover the growing trays with a “blackout dome” or an unused tray upside down over the seeds. This creates the darkness the seeds need to germinate.

If your microgreens are dirty or have a lot of soil on them at harvest time, you most likely covered the seeds with soil. And since microgreens seeds are sown very densely, as the seedlings grow, they are so close together, they carry the soil up with them as they grow.

You can also get some dirt and debris if seed hulls are still attached and dirt rides upon the leaves of the seedlings this way.

Grow Your Own Microgreens

Don’t Let These Problems Stop You!

In conclusion, Achieving microgreens success means that you have to pay attention to detail when cultivating, harvesting, and processing your greens. The plants need to be healthy, the light conditions need to be just right, and the soil needs to have optimal moisture. 

Don’t let these top 10 microgreens growing problems get in the way of growing your own nutritious microgreens. 

  • Identify the problem

  • Learn about the causes of the problems

  • Take steps to correct the problems

Do this and you’ll be on your way to a more nutritious lifestyle that both you and your family will enjoy.

Grow the best microgreens by following these troubleshooting tips. If you’re having problems growing your own microgreens, we’ve got the answers.

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