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What Causes Microgreen Mold & 7 Proven Tips To Prevent It!

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close up photo of mold growing on pea seedlings

What Causes Microgreen Mold?

The most common reasons for mold growth on microgreens are excessive watering or moisture, high humidity, poor air circulation, contaminated seeds, contaminated growing medium, and contaminated equipment.

So let’s dive in and discuss what causes mold to grow, how to identify it, and most importantly, how to prevent it from forming on your microgreens.

What Is Microgreen Mold?

Before we talk about what causes microgreen mold, we first need to understand what mold is and what it isn’t. People often mistakenly use the word mold and fungus interchangeably, although they’re related – mold is a fungus type (plural fungi).

Fungi are a type of microscopic organism that’s present all around us, even in the very air you’re breathing. It’s neither animal nor plant nor a type of bacteria. It’s an organism with its very own kingdom of classification called Fungi.

A recent estimate suggests that as many as 5.1 million fungal species exist in the world. They include molds, mildews, yeasts, rusts, smuts, and mushrooms.

So what is mold? As I mentioned above, molds are a type of fungus. It has become a common word used widely to describe all types of mold, and it’s no wonder considering there are over 100,000 mold species!

These small organisms can be white, black, blue, yellow, orange, green, or purple and live everywhere. Molds need moisture to thrive, and they reproduce through microscopic spores that fly through the air. When they land on a moist spot, they can start to grow and spread.

Here’s a wicked timelapse showing various fungi developing, specifically Aspergillus niger, Rhizopus, Aspergillus oryzae, and Penicillium.

How To Identify Microgreen Mold

Due to the overwhelming number of mold species, it’s sometimes hard to tell what fungi or mold has spread to your microgreens.

One of the most common microgreen molds we see is white mold. White mold is actually not a type of mold at all – it’s just a catch-all phrase. A lot of mold species will appear white during their early development.

The most common species of molds found in homes are Cladosporium, Penicillium, and Aspergillus. All of them may appear white, gray, black, green, or other various tints.

White mold growing on sunflower microgreens
White Mold Growing On Sunflower Microgreens

Now you don’t have to memorize all the scientific names of all these molds and fungi. But you do need to know what to look for when searching for mold. In case you do have mold growing on your microgreens, this is what to check for.

Symptoms of Fungi and Mold

Expand the following list of microgreen symptoms to view detailed information.

dead wheat seeds and sprouts with white mold
Wheatgrass destroyed by fungi covered in mycelium.

Some seedlings will emerge but most will not, which will result in sporadic growth. The growth will be slow and eventually, the resilient seedlings that did manage to sprout will succumb to the fungi infection, fall over and die.

Close up of green peas with white fungal growth
Green peas covered by mycelium.

Visible fungi on the seeds, seedlings, or grow medium that appears like spiderwebs or fluffy cotton swab balls.

Sunflower microgreens with white mold and dark spots on the cotyledons
Sunflower microgreens covered by mycelium.

Cotyledons (the first embryo leaves that emerge, usually heart-shaped) are soft, mushy, or appear water-soaked and discolored with dark spots.

Young seedlings suffering from wire stem disease
Young seedlings suffering from wire stem disease

The seedling stems are discolored, thin/pinched, and appear water-soaked. Maybe falling over due to thin strand-like stems where the seedlings are infected.

Close up photo of seedlings with rotting stems
Close up photo of seedlings with rotting stems

The stems of young seedlings will be discolored and rotting either above or below the growing medium.

Young seedling cotyledons wilting
Young seedling cotyledons wilting

Cotyledons will droop down and wilt. The leaves may turn brown or greenish-gray in color.

Close up of a hand touching rotting roots
Root rot

The roots will be mushy/slimy to the touch, stunned, or absent. They may appear brown with dark black spots indicating root rot.

Photo of foul smell from rotting pea seeds
Rotting pea seeds, covered by mycelium.

You may notice a bad or foul smell coming from the affected tray. Without good ventilation, an anaerobic (no air) condition mixed with high moisture will create a very unpleasant sulfur or rotten egg odor.

Photo of amaranth with damping off
Amaranth suffering from damping off.

You may see a crop circle-like hole affecting some microgreens while the others seem unaffected, with time the hole will radiate and eventually affect the entire crop.

Close up photo of pea seeds rotting with a foul odor
Pea seeds drenched and rotting.

Seeds rot and are soft and mushy to the touch before the emergence of the stem and cotyledons. Usually accompanied by a foul sulfur odor.

Now that you understand what microgreen mold and fungi can look like, it’s time to discuss and answer the one question all beginner microgreen growers keep asking. “Are these root hairs or mold?”

Difference Between Microgreen Mold & Root Hairs

Before you can understand the difference between microgreen mold and root hairs, you first need to know what root hairs are and what they’re not.

Illustration of a plant showing thr internal and external structure of the roots
Illustration of internal and external structure of plant roots.

First of all root hairs are not hairs, they do somewhat resemble hairs, but they’re not actually hairs like the ones you have growing on your head.

The scientific term for root hairs is transvacuolar strands or TVS for short. Root hair diameter can range anywhere from 10 µm (micrometer) to 5mm or more in size and length.

Lepidium sativum root hairs under microscope
Cress root hairs under a microscope.

Root hairs significantly increase the root surface area and the root diameter. It’s believed their purpose is to aid plants in anchorage, nutrient acquisition, and microbe interaction (Grierson, 2002).

So what’s the difference between root hairs and microgreen mold? Root hairs are tiny bright white elongated tubular extensions of an epidermal cell of a root. Molds, however, are a diverse number of fungal species that grow in multicellular structures called hyphae.

Macro photograph of Rhizopus fungus on an orange
Macro photograph of Rhizopus Fungus growth.

Most beginner microgreen growers get root hairs confused with mycelium growth and panic! Fear not! There’s a simple technique you can do to instantly confirm if it’s root hairs or fungi.

Grab a spray bottle with a fine mist nozzle, gently mist the roots, and if the root hairs disappear, congratulations, you just confirmed that they’re root hairs. However, if you spray mycelium, it will not retract or disappear!

Here’s a short video showing how Sango Radish root hairs collapse when they’re sprayed with water. If this indeed was mold it would not be affected by the water and the mold structure would be unaffected.

So keep that in mind next time you see the little fuzzy growth on your crop. Eventually, you will be able to just eyeball it without spraying because you’re going to be a boss at growing microgreens!

What Causes Microgreen Mold

white mold covering soil
Grow medium covered by mycelium growth.

As we have discussed, fungi and mold require moist, dark anaerobic environments to thrive. Unfortunately, creating those perfect conditions is all too easy while growing microgreens indoors. Let’s talk about them in more detail to better understand how to prevent them.

Excessive Moisture & Overwatering

Fungi love and require water. They absorb any and all extra water in a microgreen tray to survive and spread. As microgreen trays are shallow it’s all too easy to overdo it when it comes to watering your crops.

Arugula microgreens rotting due to over watering
Over watered Arugula microgreens rotting.

Poor Air Circulation

As microgreens are grown indoors, they need good air circulation. Microgreens are more susceptible to fungi as they’re grown on cramped shelves. Without good air circulation to help them dry between watering they provide the perfect breeding ground for fungi.

High Humidity

High humidity can worsen microgreen mold problems. If not controlled correctly will lead to widespread fungal or bacterial problems.

Contaminated Soil & Equipment

It’s all too easy to overlook your growing medium and equipment. Your growing medium itself can be the root cause of fungal problems. While your growing medium may have good microorganisms, it can become contaminated before it lands in your tray.

Hand holding fungi contaminated soil
Fungi infected soil.

Poor Drainage

Poor water drainage can lead to excess moisture and humidity, allowing microgreen mold and fungi to grow and thrive. Poor water drainage can be caused by a lack of drainage holes, dense-growing medium, and deep microgreen trays.

How To Prevent Microgreen Mold

Fungi and mold problems are unavoidable, but there are proven strategies to stop them from forming on your microgreens, so let’s get started and discuss how to prevent mold on microgreens.

Control Moisture & Avoid Over-watering

Water being sprayed over radish microgreens
Daikon, China Rose and Rambo Radish being watered.

Controlling moisture and avoiding overwatering is the most important step when growing microgreens. During the germination stage, you only need to lightly spray the seeds with water until the seed pushes out its radical.

Once the radical reaches the bottom tray you immediately switch to watering from the bottom only by adding a cup of water to the bottom tray every 12-13 hours.

Improve Air Circulation

two electric fans running on a microgreen growing shelf
Dual electric fan setup.

All plants need air circulation, otherwise, fungi will quickly start to develop and wreak havoc. Improving air circulation can be achieved by adding more fans to the grow rack, adding auxiliary fans to the grow room, or simply cracking a nearby window to allow some fresh air into the room.

Control Relative Humidity

To effectively control humidity in your grow room it’s important to have an understanding of the relative humidity levels inside your grow room. You can do this by investing in a digital hygrometer, which provides accurate readings.

I use and recommend the ThermoPro TP50 Digital Hygrometer because it quickly detects sudden changes in humidity making it ideal for environments with fluctuating moisture levels.

With its high accuracy and fast refresh rate, it provides up to date readings with precision of ±2–3%RH and ±1°F. Additionally, this device keeps track of the highest and lowest recorded levels, ensuring a healthier indoor grow environment. It includes a tabletop stand, magnetic back and the option to switch between °F and °C.

Hand holding a ThermoPro TP50 Digital Hygrometer
ThermoPro TP50 Digital Hygrometer

Controlling humidity in the grow room is easier than most people think! The cheapest method is to open up a nearby window and allow fresh air inside the grow room.

Alternatively, if you have no windows you can purchase a cheap dehumidifier to help when the humidity of the room gets above 70% RH.

Sterilize Equipment & Medium

Woman washing gardening trowel on grass
Washing gardening trowel.

Most new microgreen growers ignore this step, which can cost you a lot of time and money if left unchecked. After using any equipment that comes into contact with your grow medium you need to wash and clean it.

These include your grow trays, gardening trowel, gardening fork, knives, scissors, shovels, buckets, wheelbarrows, etc. If you never clean your equipment you could be inadvertently transferring fungi from one area to the next.

Improve Drainage

Make sure you have trays with enough drainage holes. If your inner tray that holds your grow medium only has a few holes you may be setting yourself up for a disaster.

I personally recommend Bootstrap Farmers 1020 Extra Strength Trays that have a mesh bottom, these trays will last you a life time, they even come in different colors!

multi-color 1020 trays from Bootstrap farmer
Bootstrap Farmers wicked colored 1020 trays!

If you already own trays that have a few holes you can always grab a drill and drill some additional holes to improve drainage.

Control Grow Room Temperature

Maintaining the appropriate moisture levels and temperature range is crucial for cultivating healthy microgreens. For optimal growth, a thermometer is a must-have tool. The TP50 Hygrometer/Thermometer is a great solution, it keeps track of both temperature and relative humidity.

The ideal temperature range for microgreens is between 22-25°C (71-77°F). If your growing area tends to be cooler than this range, using a heater to raise the room temperature to the appropriate level is recommended.

If your grow room tends to be warmer, using an air conditioner can help regulate the temperature and maintain a balanced environment.

By monitoring and adjusting the temperature as needed, you are providing your microgreens with a comfortable environment for them to thrive and produce excellent results.

Remove & Dispose of Infected Crop

It is crucial to address the presence of mold and fungi on microgreens to maintain a healthy and thriving crop. When you find a tray affected by fungal growth, it’s critical to take prompt and effective action to prevent further contamination. One of the primary steps you should take is immediately to remove and dispose of the infected crop.

While folks may suggest trying to salvage the affected tray using remedies like hydrogen peroxide or various anti-fungal sprays, you should consider whether investing time and effort into this approach is worth it.

When faced with a fungal infestation, prioritizing the well-being of your entire microgreens setup becomes crucial. Instead of trying to salvage a compromised tray, it’s often best to be cautious and dispose of the affected crop promptly.

This precautionary measure prevents fungi from spreading to neighboring trays and protects the overall health of your microgreens cultivation environment.

While it may seem tempting to try different anti-fungal treatments in the hope of saving the tray, you need to consider the potential advantages compared to the risks. Microgreens are delicate and sensitive plants, and using chemicals or treatments can sometimes cause more harm than good.

Additionally, the time and effort spent trying to fight off the fungal infestation might outweigh the benefits of simply starting fresh with a new batch of seeds.

Frequently Asked Questions

Why are my microgreens growing mold?

Microgreens can grow mold due to excessive moisture, high humidity, poor ventilation and air circulation, contaminated seeds, contaminated growing media or contaminated equipment and grow trays.

What causes mold to develop on my microgreens?

Mold development is primarily caused by high humidity, overcrowding, or inadequate air circulation.

How can I prevent mold from forming on my microgreens?

Prevent mold by ensuring proper drainage, adequate air circulation, and maintaining ideal humidity levels.

Are there specific types of microgreens that are more prone to mold?

Some microgreens, like basil and cilantro, are more susceptible to mold due to their moisture requirements.

Can I still eat microgreens that have mold on them?

It’s best to discard microgreens with mold, as some molds can be harmful if ingested.

What are the signs of mold on microgreens?

Signs include white fuzzy, discolored growth, a musty odor, and a slimy texture.

Is it safe to eat microgreens with white mold?

It’s generally not safe to consume microgreens with any type of mold, including white mold.

What is the impact of mold on the flavor and texture of microgreens?

Mold can negatively affect the flavor, texture, and overall quality of microgreens.

Do different growing mediums affect mold growth on microgreens?

Choosing the right growing medium with good drainage can help reduce the risk of mold.

Can mold on microgreens be harmful to my health?

Yes, some molds produce mycotoxins that can be harmful when consumed.

How does humidity and moisture levels in the growing environment affect mold growth?

High humidity and excessive moisture create favorable conditions for mold growth. Keep humidity below 70% RH.

What are the best storage practices to prevent mold after harvesting microgreens?

Store harvested microgreens in the refrigerator in a sealed container with a paper towel to absorb excess moisture.

Are there any natural or organic methods to prevent mold on microgreens?

Natural methods include using neem oil, cinnamon, hydrogen peroxide or apple cider vinegar as mold deterrents. But I recommend you prevent it from forming in the first place!

How can I control the airflow and ventilation in my microgreens setup to reduce mold?

Use fans or open windows to promote air circulation in the growing area.

What are the most common mistakes that lead to mold issues with microgreens?

Common beginner mistakes include over-watering, overcrowding, and inadequate ventilation.

Do I need to use any specific fungicides or treatments to prevent mold in microgreens?

It’s best to avoid chemical treatments and focus on preventive measures like proper care and sanitation.

What is the role of proper sanitation and cleanliness in preventing mold in microgreens?

Keeping all equipment and growing areas clean helps prevent mold contamination.

Can mold issues be a result of contaminated seeds or growing trays?

Yes, mold can be introduced through contaminated seeds or unclean trays.

Are there specific temperature ranges that are ideal for microgreen growth to prevent mold?

A temperature range of 22-25°C (71-77°F) is generally ideal for microgreen growth and mold prevention.

Is it normal for mold to appear during the germination phase of microgreens?

Mold during germination can occur, but it’s crucial to address it promptly to prevent further issues.

How do I identify the different types of mold that can affect microgreens?

Identifying molds by appearance can be challenging, it’s safer to discard any moldy growth.

What is the role of overwatering in mold development on microgreens, and how can I avoid it?

Over-watering can create excessively damp conditions, promoting mold growth; water sparingly to prevent it.

Are there specific air circulation systems or fans that work best for mold prevention in microgreens?

Oscillating fans or small, quiet fans can improve air circulation in your growing area.

How can I troubleshoot mold issues when I'm already experiencing them with my microgreens?

Isolate affected trays, improve ventilation, reduce watering, and consider using natural mold deterrents.

What role does proper drainage play in mold prevention for microgreens?

Good drainage helps remove excess moisture, reducing the likelihood of mold growth.


Now that you’ve learned what causes microgreen mold and how to prevent it, it’s time for the hard part… doing it! You can totally do this! Have fun, experiment with the process, and learn as you go, it’s an incredibly rewarding journey growing microgreens. To get you started check out some microgreen types you can grow today.

If you get stuck, or can’t figure out why your microgreens are not growing feel free to write your issue in the comments below, or, join my Mirogreen Silo Green Thumb Tavern group and discuss your growing woes there, see you there!

And remember, Keep Your Hands In The Dirt! 👨‍🌾

Comments (6)

Very good information

Glad you enjoyed it, and found it helpful. ‍

Joan Mangiaracina

Great info, I learned a lot about mold & fungus! Thanks!!

Appreciate your feedback! It’s great to know that you found my blog post about preventing mold and fungus in microgreens helpful❤️. If you ever have any more questions or need additional information, please don’t hesitate to reach out. All the best in your microgreen growing journey!

My arugula always grows fungus! This is very good information and thank you so much for your help!

You’re very welcome! I’m glad to hear that you found the information helpful. Dealing with fungus on arugula can be a common challenge, but with the right care and precautions, you can enjoy healthy and delicious arugula all year round! If you have any more questions or need further assistance, feel free to ask. Happy gardening!

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