How to Tell if Microgreens Went Bad: 9 Signs to Look For

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Microgreens pack a delicious and nutritious punch that many love. Whether you want to use your microgreens on a salad, as a garnish, or incorporate them into a dish, many love the taste and added nutrients that come with these tiny but mighty veggies. While they are fairly easy to grow, you may find yourself having problems with getting the result you want.

If you are considering starting growing microgreens or have already done so and experience problems, we are here to share more about what are the common microgreens problem you should look for and how to solve them! 

How do you tell if your microgreens have gone bad? The most common reason why microgreens go bad is due to mold or fungus. In this blog, we will discuss this and eight other ways that you can tell if your microgreens have gone bad.

  • Mold or Fungus
  • Slow Germination
  • Yellowish Coloring
  • Clumpy Growth
  • Weak Plants
  • Plants Falling Over
  • Uneven Growth
  • Dirt Present at Harvest
  • Root or Stem Rot 

How to spot bad microgreens is a commonly asked question amongst those who want to grow and cultivate their own greens because these tiny plants can cause you some challenges. Continue reading to learn more about what may cause your microgreens to go bad and what you can do about it.

How Do You Know if Microgreens Have Gone Bad?

Microgreens make a great plant to grow whether you are an avid grower, or you are just starting out with your little garden. They can be grown both indoors and outdoors with relative ease on your part. The main thing to keep in mind is that your greens will need an adequate amount of sunlight and fairly routine care. 

However, once you have planted your microgreens, there may be a few issues that you run into that will need to be addressed. If you have noticed your microgreens are not performing well, have a weird smell, or simply look off, they may have gone bad. Some common things to look for when it comes to microgreens and if they have gone bad are:

1. Mold or Fungus

This is perhaps the biggest issue that microgreen growers run into on the regular and one of the biggest reasons that your crops may not be performing well. Most microgreens will have root hairs around the main root of the seed, which you should mistake for mold. Instead, mold will look more like a spiderweb crawling across the surface of the growing media. 

Most often, the mold will start in one small area and be a wispy ball. However, the mold can expand quickly and take over the growing media in only a couple of days. Before long, the mold will make its way up the stem of the plant and can ruin your entire crop in no time. 

Luckily, there are some ways to avoid mold buildup and even deal with it before it causes a major problem. Some notable solutions are:

  • Always clean your trays before planting your microgreens.
  • Decrease your sand density in future trays. This is especially true if you are planting seeds that are considered mucilaginous. 
  • Decrease the humidity around the plants by increasing the overall air circulation. 
  • Lower the seed density in future microgreen trays.
  • Some add grapefruit seed extract and water to the plants as an organic solution. 

RELATED: Why Microgreens Mold and How to Prevent It

2. Slow Germination

Another noticeable factor that can tell you that something is wrong when it comes to your microgreens and their growth is if they are slow to germinate. Since microgreens are picked very early, you should see germination within two to four days. Though some seeds may take a bit longer, if you are noticing a large time increase, something is most likely wrong. 

To help speed up the germination process and ensure the safety of your plants, you may want to increase the moisture in the tray. If you find that it is drying out, this means you should spray the tray more often. You can also do a germination test with some of the seeds in a wet paper towel. See this video to learn how to do it:

3. Yellowish Coloring

If you have noticed that your microgreens are appearing somewhat yellow, this is a sign that something may be going wrong. Before taking the blackout dome off of the microgreen trays (an important part of growing) or moving them from a dark space, the seedlings will mostly all be yellow. This is because they have not taken in the light necessary for photosynthesis to occur. 

However, if you continue to see this yellowish hue on your plants, it could mean something is wrong. You can start to remedy the problem by moving the greens closer to a stronger light source. You should note that the color of your microgreens will change as they are exposed to light. 

You can also take the blackout dome off of the trays earlier on to avoid this strong of a yellowing. 

4. Clumpy Growth in Microgreens

A big part of growing your own microgreens is planting the seeds, which need to be spread out in the trays appropriately. Unfortunately, it can be difficult to get an even spread, and this can lead to issues with your greens. If you plant the seeds to densely, they can actually clump together. This can be an even bigger problem with mucilaginous seeds.

The problem occurs when the plants begin to sprout because they will push the seedlings up into the air, which will then suspend the roots. This can not only bring dirt up with the plant but can also make it hard to harvest. Also, plants that result from these clumped seeds are often very uneven when grown. 

When planting mucilaginous seeds, you need to pay special attention to spreading the seeds out evenly around the tray. Also, the next time you plant, you may want to decrease the seed volume per tray to avoid seed clumping. Some common mucilaginous seeds, which form a sticky gel coating when wet are:

5. Weak Plants

While microgreens are always going to be rather small, they should not appear overly weak. This can be one of the hardest things to pinpoint when it comes to determining if your greens have gone bad but should be dealt with accordingly. If none of the other common issues on our list seem to be at fault, the weakness may be caused by a lack of moisture control.

You always want to ensure that your microgreens are neither too wet or too dry when growing. If you don’t properly prepare the seeds, take the blackout dome off to early or too late, or are not controlling water levels, plants can easily become too weak. 

Some ways that you can increase the strength of the greens or avoid this issue in the future are:

  • Read the packets carefully and ensure you are meeting the plant’s needs.
  • Make sure you take off the blackout dome or remove them from the dark space at a crop-specific time and do additional research on which time seems best. 
  • Some crops require that they struggle to thrive to grow stronger; this is when the blackout dome is flipped on top of them.
  • You should make and stick to a good watering and misting schedule for your plants. 

6. Plants Keep Falling Over

Going hand in hand with weak looking microgreens, a similar issue is when your plants keep falling over or even wilting on top of each other. This can cause the plants to begin to decompose and can mean they are no longer edible to the grower. Often, plants near the center of the tray will lean, but if you notice a large number leaning, it is time to act. 

Some common reason that microgreens lean is because of a lack of sun and water. You want to ensure that the entire tray is getting watered regularly and adequately. Also, the plants mustn’t work to get proper sunlight. If you don’t have a place where they can get an even amount of light, rotating them to get adequate sun is also very important. 

RELATED: 10 Reasons Your Microgreens Are Wilting

7. An Uneven Growth Pattern

Another issue you may notice that can lead to your microgreens going bad is if the growth is uneven throughout the tray. Often, the plants will grow well on one side of the tray and be taller in height. However, some of the plants may be noticeably shorter on another side of the tray.

Similar to seeing plants that are falling over, plants with uneven growth are usually caused by them needing additional sunlight. Seedlings will naturally grow toward the light, and limited sunlight can lead to one area growing better and taller than another. You will want to either provide artificial light to the shorter side or rotate your trays regularly to keep light on all the greens. 

8. Dirt Present at Harvest

One thing that makes harvesting your microgreens more difficult is when they have dirt present. When the day comes to harvest your greens, it can be really exciting, and you cannot wait to eat your hard work. However, when you cover your seeds in a layer of soil, they will grow with dirt on the leaves. 

While using a layer of dirt over the seeds can increase the germination rate, it can complicate the harvesting process. At times, removing this small layer of dirt can be extremely difficult and annoying. If you don’t want to worry about this dirt, you can spread out the seeds more evenly, cover them with a layer of loose soil, then finish the planting with a layer of compacted soil. 

9. Root or Stem Rot

Another common issue that can cause the microgreens to go bad is rot and stem rot. This is caused by heat stress, high humidity, and a lack of ventilation. These factors, mixed with inconsistent airflow, can lead to air deficiency and root rot. The most common way to know if your microgreens have this rot is if you notice a bad or swampy smell. 

As soon as you notice the smell, inspect your plants to see if the rotting issue is present and begin to remedy it. If you do not deal with the rot quickly, it can spread quickly, and the entire batch of greens will need to be thrown away. Microgreens with root rot will not be safe to consume and must be thrown out. 

Can You Eat Microgreens That Have Gone Bad?

Now that you know more about what makes microgreens go bad and how to handle them, you will also want to know more about safely eating your greens. Eating microgreens are generally safe. However, there can be bacteria growth and then you should not eat them.

If you notice mold or root rot on the greens upon picking them, you do not want to eat them. If any of your trays have mold present, you must throw out these greens. Go through the reasons why mold may appear and next time you know what to do to be successful. 

If you have any doubt if your greens have gone bad, what you can do is to cook them fully. Most negative microorganisms or germs present will be killed out when the microgreens have been washed and cooked. 

Are Your Stored Microgreens Bad?

Once you pick your microgreens, you want to store them safely. However, they can also go bad quickly once they have been picked, and you want to eat them within a few days. Some common ways that you can tell if your stored microgreens are bad are:

  • The leaves are shriveling, and the water content has dissipated. These can be eaten, but they will not be as fresh tasting or pack as much nutrition.
  • They begin to have a smell. As microgreens go bad and start to decay, they will give off a foul odor that is much stronger than any odd smells they may naturally have. You can easily smell the difference in decaying produce and fresh greens. 
  • The stems on the plants become mushy. When decay begins, one of the first things that you will notice is that the stems become mushy. 

You can by simple means ensure that your microgreens will stay healthy for longer. One of the main reasons for stored microgreens to go bad is that they are not properly contained. You should always place them dry in a sealed container. If you store them wet, they will quickly go bad and you will experience them becoming mushy. 

Some microgreens you may want to wash before you store them. This can be for example microgreens planted in soil. If you cut them close to the medium you may get some soil between the stems and leaves. If you do wash them, ensure to dry them before you put them in a container. Use a paper towel and let them dry and you should be good to go and have your microgreens lasting for longer.

RELATED: The Best Way to Store Microgreens After Harvest


Microgreens are simple to grow and that is why they are becoming immensely popular to grow at home. There are so many benefits that come with growing them yourselves and it is amazing to enjoy a harvest after seeing the progress of your work. 

However, even though they are easy to manage, they are delicate and susceptible to harsh conditions. You may experience some challenges as described in this article. Now that you understand what issues might be causing your microgreens to go bad, you are in a great position to avoid them and be successful from start or you know what to fix as you grow your next crop. 

Microgreens Corner
Microgreens Corner
We are Janette & Jesper, and we love microgreens.


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