How To Get Rid Of Mold On Seedlings


Gardeners love the excitement of watching trays of seeds sprout and grow into healthy seedlings.

Unfortunately, many gardeners don’t know what to do when they see mold on seedlings.

Once you know what causes mold on seedlings and how to eradicate the problem, your garden will look better than ever!

In this guide, I’ll help you understand how to handle mold on seeds, seedlings, and potting trays and soil.

Everything to Know About Mold On Seedlings

Mold is a persistent problem when gardening, especially when you are starting seeds indoors. Mold is everywhere, so it’s easy for it to take up residence in your seed trays.

The same moist and warm conditions that plants need to grow also encourages mold to form. Stopping mold before it can take over your seed trays is critical if you want all your seeds to germinate and grow to maturity.

Related | Best Seed Starting Trays

To help you better understand the mold on seedlings issue, check out the answers to these common questions below.

Will Moldy Seeds Germinate?

You open a pack of seeds and find mold growing on the surface. Are these seeds unusable?

The answer is that as long as the seed’s outer casing is still firm and not mushy, the interior of the seeds may be perfectly fine.

Related | How Long Does It Take For Seeds To Sprout

You never want to introduce any molds or fungi to your potting trays, so you will need to clean them before planting moldy seeds.

The best way to clean moldy seeds is to first spread them out onto a tray and mist them with any of the following:

  • Distilled white vinegar
  • Hydrogen peroxide
  • Isopropyl (rubbing) alcohol

Keep misting and stirring up the seeds until all the sides are damp. 

Spread the seeds back out and set them in direct sunlight. The liquid should evaporate off the seeds quickly but will have enough time to disinfect and kill off any mold spores.

There is no guarantee the germination rate of moldy seeds will be normal, so expect fewer of them to sprout and hope for the best.

Related | How To Start Seeds In Paper Towel

Is Mold Bad For Seedlings?

Yes, mold is bad for seedlings if you don’t catch or treat it right away.

Having to toss out a full seedling tray because mold has taken over is depressing, so don’t let it happen!

There are several types of mold and fungi that attack seedlings:

Having a basic knowledge of the types of mold and fungi that you may find in your seedling trays can help you identify which strains are causing you grief.

Not all molds directly affect the seedling. Many molds are feasting on the damp organic matter in the soil.

The problem is that even “plant safe” mold will deplete the nutrients in the soil the seedlings need to survive.

This is why you need to immediately remove mold, as it is still dangerous to the growth of your seedlings. 

What Is White Fuzzy Mold On Seedlings?

white fuzzy mold on seedlings

White fuzzy mold on seedlings is not the type that causes blight or damping off, which causes the plant to flop over at the base of the stem.

Once damping-off hits your seedling tray, there is no way to save the plants.

The white fluffy, fuzzy mold that you see on your seedlings is most likely a saprophytic fungus. The mold isn’t an immediate danger to your seedlings, so you have time to treat the invasion.

How To Get Rid Of White Mold On Seed Starting Soil

Getting rid of white mold on seed starting soil is a relatively easy four-step process and needs to be taken care of so your seeds can germinate.

  1. Start by using a spoon or knife to scrape the mold from the surface of the soil. Get as much as you can, and dump the moldy soil into a small plastic bag you can place in your outdoor trash receptacle to keep the spores away from your growing area.
  2. The second step is to give your seedling trays some air. If you have plastic covers over the trays, prop them open with a popsicle stick or pencil on one end. Venting will allow excess moisture to dissipate and makes it more difficult for mold to regrow. If your seeds have sprouted, you may be better off leaving the lids off entirely to keep humidity levels on the soil lower.
  3. The third step is to turn off any warming pads under the tray, as the mixture of heat and moisture allows the white mold to flourish. 
  4. The final step is to give the soil in the trays a chance to dry out, as excessive moisture is the main cause of white mold growth. Place the trays in a well-ventilated area or set up a fan to blow across them. Keeping soil moisture in balance for seeds to sprout can be tricky. You need the soil to stay consistently moist but never too wet. You are better to err on the side of caution and wait for the soil’s very top layer to become dry before you water again. Misting the tray offers more control than using a watering can.

Reusing old soil with a white mold issue is safe if you spread it out thinly on a tarp or piece of cardboard and let it bake in the sun for a day. The heat and light will kill off any remnants of spores hiding in the soil.

Tips to Keep Mold at Bay

To keep while mold from returning, provide good air circulation over your seed trays by running a fan.

Consider watering your trays from the bottom instead of the top. Bottom watering brings moisture much faster to the roots but keeps the surface of the soil dryer so mold can multiply as quickly.

Just remember never to let the trays sit in water for any longer than 20 minutes, or they’ll absorb too much water and soak the soil anyway.

How Do You Get Mold Out Of Seed Starter Pots And Trays?

The best way to get mold out of seed starter pots and trays is to sterilize them before use.

I like to make a batch of cleaner made of 90% water and 10% household bleach and put it in a large plastic tub.

I toss in all my trays and pots I use for seeding and let them soak for a few hours. I prefer this method over spending time scrubbing out and rinsing each seeding container.

Since the plastic likes to float to the surface, I use some of my weighty go-to gardening hand tools like trowels, rakes, and cultivators (these tools need cleaning too!) to hold them down or use a couple of large rocks. 

You want to ensure all the nooks and crannies in the trays get exposure to the bleach solution, so any hidden mold, fungi, or bacteria die.

After soaking, rinse the items well with water and let them air dry before use or storage.

Fungicide For Seedlings

Novice gardeners may wonder if using a fungicide for seedlings is safe and effective in keeping molds off their trays.

The answer is that yes, fungicides do work to kill off mold and fungi in the soil before they can harm your seedlings.

You can purchase a broad-spectrum fungicide to use as soon as you see even the smallest signs of mold growth in your seed trays or as a pre-treatment for seeds before you plant.

The problem is that many fungicides use harmful synthetic chemicals that are bad for the environment in general. 

There are recipes online for natural DIY fungicides you can create at home, but some ingredients aren’t as effective as others against all the different strains of mold you may encounter as you garden.

Here is a quick rundown of the pros and cons of using a fungicide for seedlings:


  • Higher seed germination rate
  • Robust growth as the plant isn’t fighting with fungi for nutrients
  • Higher crop yields


  • Fungicides also kill off beneficial microbes that break down organic matter into nutrients plant roots can absorb
  • Fungicides can add to soil and water pollution problems
  • Some fungicide chemicals are harmful to human health

The key is to use fungicides correctly to mitigate any damage to your plants and the environment.

In Summary

There isn’t any need to panic if you see mold on seedlings.

When you use the information above, you can decrease mold issues when starting seed and getting seedlings ready for transplant.

Using the right gardening techniques to combat mold will enable you to enjoy higher seed germination rates and vigorous seedling growth, so next season’s garden will be a complete success!

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