How To Get Rid Of Mold On Microgreens (easy fixes)

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Microgreens are tiny seedlings that abundantly proliferate, taste great, and pack a powerful nutritional punch. However, if you don’t know how to get rid of mold on microgreens, and if they are not cared for and maintained properly, these tiny plants can spoil faster than a glass of milk left outside in an Alabama summer.

Generally, one teaspoon of 3% food-grade hydrogen peroxide mixed with 2 cups (16oz) of water gently misted over the affected area effectively removes mold from your microgreens. Replace one regular watering by spraying this mixture conservatively, aiming for the base, so this mixture doesn’t contact the leaves and burn the plant. Then, put your microgreens in direct light to allow the area to dry. 

closeup of person holding three paper wrappers in hands of different microgreens

In this article, we’ll dive deep into how you can get rid of mold in your microgreens to better enhance your harvests, along with essential steps to reduce its occurrence so you can get back to the best part: eating them!

Humble Highlights

  • Discover the 4 common ways mold forms in your microgreen containers and how to avoid each so you can start providing stable temperatures and healthy ventilation to your plants.
  • Save money by learning to spot mold immediately so you can treat it BEFORE it crushes your entire crop.
  • Discover why removing mold from your microgreens is easier than you think PLUS 8 specific ways to stop it in its tracks!

What Causes Mold In Microgreens

There are four common ways mold grows on microgreens: excess moisture, seed spacing, lack of air circulation, and high humidity. Microgreens that are susceptible to these general causes become stressed, sick, and ultimately more susceptible to moldy conditions. 

what causes mold in microgreens
This spidery mold growth seen on these developing microgreens is something to be avoided. If left untreated, mold can spread quickly across your trays and infect your entire crop.

Simply put, mold is a type of fungus. Moreover, these tiny organisms are neither animal, plant, nor bacteria but instead organized under their biological kingdom of classification called Fungi. They come in a virtual rainbow of colors and need continual moisture to survive and multiply. 1

If you are growing your greens in soil, hydroponically, or another alternative growing medium, mold can become a real problem if not caught early. Therefore, it’s always good practice to be an efficient observer of your growing trays to detect any signs of trouble and improve your growing process to eliminate this issue immediately.

Here are four common factors that may be the mold-causing culprits in your microgreens growing area. 

Overwatering Your Microgreens

Overwatering microgreens at any stage during the growing period can be a recipe for disaster, as mold can result. Mold loves moisture-rich, stagnant, and water-logged environments. And so, correctly watering your microgreens becomes more of an experienced art than one of science. Sure, your greens need water to germinate, but too much of it breeds unnecessary trouble that can destroy your crop.

An excellent practice to follow when growing microgreens is to provide a wet environment, not a saturated one. Your plants will love the fact you keep their germinating roots moist while preventing mold from forming by offering a properly draining growing medium.  

Bottom watering, for example, is a good option if you use an alternative growing medium like coco coir. However, this watering method can also work successfully using soil. 

Bottom watering, or reverse watering, is when you place your microgreens tray (with drainage holes for roots) into another tray (without holes) that contains water. The water in the bottom tray is soaked or wicked up by the developing roots of plants within the growing medium. This method effectively neutralizes any excess moisture that would typically form around the densely packed stems of your microgreens, therefore decreasing the likelihood of mold forming.


Interestingly, microgreen seeds sprout from the same seeds you would grow in the vegetable garden. However, when sowing these seeds as microgreens, you are spacing these seeds much closer together. And because you are densely seeding over a particular growing area within a moist environment, it can cause several common fungal conditions, such as damping off, that can be catastrophic to your budding greens.

hydrogen peroxide for microgreens
Microgreens seeds of radish, peas, and watercress await planting.

Damping off is a fungal (mold) infection that often occurs in new seedlings, making your young, unprotected microgreens a likely target. Damping off occurs in moist and cool conditions and can potentially wipe out an entire crop of micros if not appropriately treated and managed. 

In order to cut down the chances of mold or fungus forming in your trays, ensure you are not overseeding your growing area. Whether you grow your micros in soil, a grow mat, or another alternative medium, follow the instructions on the back of each microgreen seed bag to maintain the correct upright seeding density for your crops.  

Also, when sowing your micro seeds, spread them as evenly as possible over your growing surface. Even if you soak your seeds prior to sowing, as some varieties recommend, ensure your seeds are dry before spreading them throughout your growing medium so they don’t clump or cluster together.

Humble Tip:

Mold, fungus, or any harmful pathogen can also lurk within your used growing trays, tools, or the environment itself. When reusing your trays or tools, brush or tap out any remaining debris, rinse with warm water, and then spray each tray with either food-grade 35% hydrogen peroxide or a general disinfectant that contains at least 70% alcohol. 

Excess Moisture And Temperature Within The Growing Medium

Moisture is another common offender when it comes to mold formation within microgreens. Everything from the climate in which you live to the environment where you grow your micros will have some effect on moisture. Even microgreens themselves create moisture through transpiration, a process where water evaporates from their tiny leaves.

Although most microgreens grow well at room temperature, keeping the temperature range around 75°F is best for optimal plant health and humidity control. For this reason, consider a dedicated growing area for your plants where the temperature and moisture can remain relatively constant. 

microgreen mold prevention
Using a basic hygrometer to measure the humidity of your microgreen growing area is an excellent and inexpensive idea to monitor the microclimate your greens are growing within.

Check Lowest Prices On Hygrometers Here

One of the easiest ways to measure the humidity is to invest a few dollars into a hygrometer, which measures the amount of water vapor circulating in the air. If your humidity is consistently above 35-40% within your growing space, it’s best to lower this number with a dedicated dehumidifier. A dehumidifier filters excess water from the air and recycles this now dryer air back into the environment, but fortunately, it does not affect the temperature. 

Check Lowest Prices On Dehumidifiers Here

Humble Tip:

Growing microgreens outside can be done successfully. However, variables such as quality of light, temperature swings, unpredictable weather, and the usual garden pests may provide unique challenges. Growing indoors provides a better environment and better control over the quality of your crop and your degree of likely success. 

Poor Ventilation

Just as mold enjoys stagnant water and moisture, it equally likes stale air and high temperatures. When growing microgreens, it is wise to ensure you have some means of moving fresh air over the growing canopy of your microgreens.  

An excellent complement to providing ventilation to your crops is an oscillating fan. An oscillating fan simulates natural outdoor airflow and prevents your micros from getting windburn, so long as you don’t point the fan directly at your microgreens for long periods. 2

Check Lowest Prices On Oscillating Fans Here

Another good ventilation option is a fan extractor. The name sounds too industrial for my liking, but it’s the same simple system you see in kitchens and bathrooms everywhere. A fan extractor pushes stale air out and replaces it by pulling fresh air into the space and is a perfect addition to a growing area in any spare room or basement.

Check Lowest Prices On Fan Extractors Here

Microgreens Mold Or Root Hairs

Mold appears like a multi-colored fuzzy canopy, similar to a spider’s web, but one that shoots out in all directions. Root hairs, in contrast, are a natural part of the seed germination process. Root hairs have fine, pointed ends to absorb moisture from your growing medium and form a fuzzy spot at the base of the plant. 

microgreens mold or root hairs
Although these broccoli seedlings may look like they are covered in mold, they are actually sprouting root hairs which are a part of the seeds’ natural germination.

And while many microgreens growers can easily mistake mold for root hairs, it’s especially misidentified by those who are just starting. However, there are several steps you can take that help determine whether or not your microgreens are spouting mold. 3

Step 1 – Observe Fuzz Location 

Mold typically starts in the middle of your tray or pot since that’s where most moisture pools after watering. If you find that only the center of your growing area has this spidery fuzz, not the sides or edges that dry out faster, you may likely have mold. 

However, if you see uniform white fuzz or fur throughout your growing region, these are likely simple root hairs extending from the germinating seeds into your growing medium. 

Humble Tip:

Mold is also commonly located above the growing medium, on top of the soil, or between the budding microgreen stems. Conversely, root hairs only form around the base section of the seed itself.

Step 2 – Spray Your Seedlings With Water

A simple test you can perform to tell the difference between mold and root hairs is spraying water over the identified areas. Once misted, root hairs will nearly vanish on contact and tend to become transparent. However, mold will not disappear, and you’ll notice the water adhering to its surface. 

Step 3 – Touch It

Yes, it may be gross, but physically touching the unknown fuzz provides another critical step to determine if mold is present within your micros. Mold will be slippery and slimy and perhaps even exhibit a spongy texture. Root hairs with be neither and are much more delicate to the touch.

Step 4 – Smell It

Another tell-tale sign will be smell. Interestingly, root hairs will not exhibit any odor whatsoever. Mold, however, tends to smell slightly fruity or musty. Gently whiff the air towards your nose above the concerned area to distinguish the difference.  

Remember, lessening the chances of mold sprouting up in your micro trays comes down to implementing systems that contain it in the first place. And I’ve included a fantastic step-by-step video below detailing how you can do just that.

How Can I Get Rid of Mold From Microgreens?

Mold can be a significant problem for microgreens growers and can increase quickly on these tiny plants if not addressed quickly. Prevention is always the best remedy to keep mold from taking root in your microgreens space. Ensure your microgreens environment is as sterile as possible to give your sprouting plants the best chance throughout each growing cycle. 

how can I get rid of mold from microgreens
Healthy and mold-free trays of microgreens ready to harvest.

The best mold prevention method you can follow is controlling your space as much as possible. And although growing micros outdoors are possible, you’ll need to factor in many uncontrollable variables like temperature, pests, and weather that may impact your plants and, ultimately, your success.

Follow these easy steps to prevent mold growth and reduce the chance of ruining your microgreens. Additionally, for safety reasons, I recommend you always wear gloves and appropriate eye-wear when treating your greens for mold. 4

Hydrogen Peroxide With Water

Gently spray equal parts food-grade 3% hydrogen peroxide (H2O2) and water to the affected area of your tray to remove mold. Although this may be one of the most common ways to remove mold from a live microgreens environment, depending upon the variety of mold and how extensive it may have become, there may be more to be done. 

Use caution in spraying this solution, as even a less concentrated hydrogen peroxide, like 3%, tends to burn your delicate microgreens. Instead, begin at the base of the plant or, even better, the growing medium where the mold is present. And again, spray only the affected parts unless the mold is rampant throughout the tray.  

microgreen antifungal spray
Spraying your microgreens with a 3% hydrogen peroxide solution is a great way to decrease mold that may be overtaking your containers.

Even with treatment, there may come a time when mold has wholly overtaken your entire tray despite your best effort. In this case, the best practice is to throw out your crop and start fresh. But all is not lost. Because microgreens have a short life cycle, you’ll be set back only a few short weeks.  

Moreover, if you are an organic gardener, the United States Department of Agriculture has provided a list of approved organic pesticides, and hydrogen peroxide makes the cut. That’s because hydrogen peroxide (H2O2) breaks down naturally into oxygen and water. 

Check Lowest Prices On 3% Food Grade Hydrogen Peroxide Here

Humble Tip:

The 3% hydrogen peroxide you use to treat mold for your microgreens is the same you commonly see at your local big-box grocery store or pharmacy. Just ensure it is labeled food-grade, and you are good to go. 

Distilled White Vinegar – The Grocery Store Kind

Distilled white vinegar is another good option for treating mold on your micros. This vinegar contains about 5% acetic acid, roughly the same amount you’d find in other vinegar used for cooking. Mix two tablespoons of vinegar in 2 cups of water, then lightly spray the affected area. And like the hydrogen peroxide mentioned above, you’ll want to mist your vinegar and water solution conservatively, as applying too much may burn your tender plants. 

Humble Tip:

I strongly recommend against mixing vinegar with hydrogen peroxide. This combination creates peracetic acid, which can irritate your lungs, skin, and eyes and become toxic. Either choose vinegar or hydrogen peroxide, but not both together. 

Grapefruit Seed Extract

Grapefruit seed extract is another alternative you can try. Although not as potent as the hydrogen peroxide and vinegar options above, I suggest finding a 100% organic and natural option if you go this route. Mix 10 drops of extract with 1 cup of water and lightly mist the affected area in your microgreens growing area.

Check Lowest Prices On Grapefruit Seed Extract Here

Light And Temperature

Keeping light and temperature stable for your flourishing microgreens is one of the most critical aspects of the growing process. While too much heat can lead to mold growth with increasing temperatures, too little can cause your greens to wilt and die.

Fortunately, mold does not like light, plain and simple. There are two primary choices when providing your greens with a steady supply of light: natural direct light and indoor artificial lighting. 5

The challenge of offering your micros direct sunlight consistently can become a chore as the sun moves across the sky throughout the day. However, this is achievable as long as you don’t live in an overly humid region and can keep positioning your micros in relation to the sun.  

how to treat mold on microgreens
Because mold doesn’t enjoy light, it is an excellent tool in treating and even preventing its formation on your micro crops.

Alternatively, if growing your greens indoors, fluorescent or LED lights are great options to consider. And because indoor lighting is relatively inexpensive, it also offers you greater control over your growing environment’s temperature while providing you the option to grow year-round. In my opinion, having more control, not less, over your growing operation is the better option.

Moreover, most microgreens varieties do exceedingly well when provided 16 to 18 hours of daily light, which you cannot achieve with natural, direct light. Therefore, having a controlled indoor light source working within your microgreens system is another reason I suggest this option. 

Aside from being able to control your environment, LED lights, especially UV-B lights, can encourage the growth of additional and beneficial phytochemicals and antioxidants within some microgreens varieties, providing an even better nutritional boost to your finished crop. 

Check Lowest Prices On Microgreen LED Grow Lights

Remember, if you notice mold on your micros, spray the affected area with either food-grade 3% hydrogen peroxide, white vinegar, or grapefruit seed extract. Then, light up your tray with either direct or artificial options to help provide your plants with a healthy and vibrant environment.

Notice Title

Mold thrives in damp conditions, so when light increases, dryer conditions persist. And while mold doesn’t enjoy arid conditions, neither will your microgreens. It’s important to remember that with the more light you provide, ensure you don’t dry your greens out in the process. Keep a watchful eye on the sides and corners of your tray, pot, or container, as these areas dry out the fastest. 

Sanitize Your Seeds

Although sanitizing your seeds before sowing may not prevent mold from forming when growing, I do suggest following this practice for good overall plant hygiene and to lessen the chances of it occurring.

Seed health plays a pivotal role in any grower’s operation and is the first defense in any good maintenance regimen. Therefore, sanitizing your seeds beforehand provides the best possible start to their short growth cycle by killing any mold spores that may be present on the seed hulls’ surface.

vinegar mix for microgreens
Sanitizing your seeds with vinegar helps remove any mold that may be on the outside surface of the seed hull.

First, ensure you are purchasing your seeds from a reputable company that prides itself on quality, expertise, and reputation. Next, soak your micro seeds in undiluted store-bought vinegar for 15 minutes and then rinse thoroughly with water afterward. Finally, allow your seeds to air dry before sowing in your growing medium. 6

Humble Tip:

When storing your unused or unopen microgreen seeds, it’s essential to place them in a cool, dark, and humidity-free environment. Then, when you are ready to sow, follow the steps above to sanitize them accordingly. 

Remove Infected Areas Only If A Small Area Is Affected

This method may be the most straightforward method on this list, and perhaps the simplest. When you spot mold in your microgreens, consider physically removing the affected section, including the growing medium and plants, from your microgreen growing area. 7

However, because mold can be hard to identify early in its growth cycle, I don’t recommend this option if you’re just beginning your micro journey, simply because you may inadvertently confuse mold with root hairs, as mentioned above. 

As you become more experienced in knowing what to look for, removing sections may become an excellent option if your plants show signs of unwanted mold growth. Simply take a dull knife or scissors to cut out the affected area. Be sure to remove the plants, the soil, or whichever alternative growing medium you use to get all the mold out.

Change To Bottom-Watering Your Micros For Better Drainage 

Bottom-watering microgreens trays are a great way to improve drainage and thereby decrease the likelihood of mold. Remember, mold likes wet, stagnant environments where water pools. Bottom-watering solves this challenge by providing a healthier environment in which your greens can grow.

how to avoid mold in microgreens
Bottom-watering your microgreens provides great drainage while providing a difficult environment for mold to form.

As explained above, bottom-watering is a process involving two trays. The top container retains your growing medium and your budding plants, whereas the bottom one holds the water. Water will wick upwards through small holes or ports in the top tray, where it will be absorbed by the rooting systems of your microgreens, effectively eliminating moisture that would typically surround your plants if watered from above.

By allowing water to flow upwards and introducing moisture to your plants from this bottom-up process, mold has a more challenging time developing and spreading throughout your growing area.  

Fortunately, bottom-watering works using soil and other alternative growing mediums, like coco coir. However, coco coir is especially effective for this unique process since it can hold and store moisture for your microgreens exceptionally well.

Humble Tip:

Bottom-watering provides your greens with better drainage and helps the developing roots of your greens stay well-ventilated. Better ventilation means better exposure to oxygen and any liquid fertilizer you may choose to introduce.  

Clean Your Containers And Your Tools

Just because you’ve harvested a healthy crop of microgreens doesn’t mean mold can’t form on your containers and tools. In fact, cleaning and sanitizing your equipment between plantings is arguably the most critical time to sterilize and combat mold throughout the entire growing process.

You can employ a cutting-edge, simple, and effective process to keep your equipment clean: good old-fashioned soap and hot water. It’s essential to thoroughly wash and clean even the smallest nooks and crannies in your trays and then air and sun-dry.

what does mold on microgreens look like
Cleaning and sanitizing your microgreens trays and tools between plantings helps fight back against damaging mold.

If you feel so inclined, take another step and use one teaspoon of 3% food-grade hydrogen peroxide mixed with 2 cups of water and lightly spray your tools, trays, and containers. You may also do the same with distilled white vinegar. Mix two tablespoons of vinegar with two cups of water, gently mist, and air dry. 8 

While some micro growers opt to use bleach, I feel it is too harsh of a chemical to use in conjunction with the delicate nature of the plants you are cultivating. Fighting mold effectively should be about something other than using strong chemicals. Instead, it should be about consistently employing a sound, prudent strategy with common-sense steps outlined in this article. 

Humble Tip:

If purchasing soil as your microgreen growing medium, it’s good practice to take it out of the plastic bag it comes in and store it within a well-ventilated tub or bin. You don’t want mold or any additional fungal issues to begin growing within the pack before it’s even used. 

If you notice, the bag has several holes already punched into the side. These holes are the manufacturer’s attempt to help ventilate the soil and help release moisture before you even make your purchase. However, more air is needed to prevent mold from growing in the soil. That’s why having a dedicated bin serves you and your future microgreens in the long run. 


Mold can be a significant issue for microgreens. Fortunately, by taking some simple, preventative measures beforehand, evaluating the process, and controlling your growing space, you can lessen the chances of it forming and ruining your delicate greens.

The bottom line is that mold is abundant within the environment around us. Whether we like it or not, mold is a part of our world. Mold serves a vital purpose in the renewal of life by breaking down natural materials, such as leaves, wood, grass clippings, and Fido’s pig ear he buried in the backyard but forgot where. If mold weren’t a part of life, there wouldn’t be much of it to begin with.

Where you don’t want mold, however, is in your microgreens tray. So, the real issue comes down to your growing environment. Mold will likely take root if you provide a moist, wet, poorly drained growing medium and a moderately warm space. That’s why evaluating your growing systems and plant maintenance is essential, along with good daily observation.

When you don’t provide mold with the right ingredients to take hold, chances are it won’t. So instead, follow the steps outlined above, start small, be observant, and you’ll be on your way to growing healthy microgreens consistently and confidently.

Have you ever had any mold in your micros? What did you do to get rid of it effectively? We’d love to know your success story! Be sure to drop us a comment below and let us know what steps you took to fight back.


  1. University Of Nevada, Reno Extension – Microgreens And Produce Safety
  2. Penn State University, Extension – Growing Microgreens
  3. Wikipedia – Root Hair
  4. University Of Minnesota, Extension – How To Prevent Seedling Damping Off
  5. ScienceDirect – A Review On The Effects Of Light-Emitting Diode (LED) Light On The Nutrients Of Sprouts And Microgreens
  6. University Of Wisconsin-Madision, Extension – Damping Off
  7. North Carolina State University, Extension – Damping-Off In Flower And Vegetable Seedlings
  8. Kansas State University, Extension – Sprouting Seeds At Home Safety

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