How to Properly Disinfect Seed Trays: A Gardening Guide


Are you eager to start your gardening journey by planting seeds but concerned about potential plant diseases? Look no further! In this guide, we will explore the importance of disinfecting seed trays, learn how to prevent damping off, and discover a natural and effective method to disinfect your seed starting equipment.

Do You Really NEED to Disinfect Seed Trays?

You may wonder if it’s necessary to disinfect your seed trays before starting seeds. While it’s not always required, it’s highly recommended if you’ve previously dealt with plant diseases, fungi issues, or damping off. Disinfecting your equipment serves as cheap insurance against potential problems that can devastate your fledgling plants.

What is Damping Off?

Picture this: you plant a seed, water it, and excitedly watch as it emerges from the soil. But then suddenly, the seedling withers and dies without any explanation. This unfortunate phenomenon is called damping off. It is often caused by fungus or mold, which can affect just a few seeds or wipe out entire trays of seedlings. To prevent this heartbreaking experience, it’s crucial to take simple precautions.

How to Prevent Damping Off in Seedlings:

To safeguard your seedlings from damping off, follow these preventative measures:

  • Don’t reuse dirty potting soil.
  • Keep your seedlings warm during sprouting.
  • Water seeds or seedlings with lukewarm water.
  • Avoid crowding seedlings.
  • Provide sufficient light for seedlings.
  • Clean and disinfect pots, flats, and trays before use.

How to Disinfect Seed Trays

If you’re not a fan of using bleach, rejoice! There’s a natural alternative that is just as effective: hydrogen peroxide. Here’s a step-by-step guide on how to disinfect your seed trays without the strong odor and harshness of bleach.

Step One:

Begin by shaking out any residual soil from the seed trays and flats. If the soil is dried and crusty, you may need to soak everything in water to remove it.

Step Two:

Scrub the trays and containers with warm, soapy water. You can use natural cleaning concentrates like On Guard Cleaning Concentrate or regular soap and water. This step alone can eliminate most issues that lead to damping off.

Step Three:

Spray the trays, flats, cups, or any other equipment with a generous spritz of hydrogen peroxide. Allow everything to sit for 20 minutes, giving the peroxide time to work its magic.

Step Four:

Using a clean, dry cloth, wipe down the trays and containers. Once dry, you’re ready to plant your seeds. It’s that easy!

Seed Tray Disinfecting Notes:

  • It’s advisable to perform this project outdoors or in a well-ventilated area. If you have several trays, consider using a big plastic tub outside to avoid making a mess.
  • Leaving your seed trays to dry in the sun is an additional way to eliminate any lingering microorganisms.
  • Vinegar can be an alternative to hydrogen peroxide. You can try spraying the rinsed flats and pots with white vinegar, wiping them down, and following up with a spritz of hydrogen peroxide for added effectiveness.
  • For more details on how to set up a laundry room washtub sink, check out our informative post on the subject.


Disinfecting your seed trays is a simple yet essential step in ensuring the success of your seedlings. By following the provided guidelines and using hydrogen peroxide, you can prevent damping off and other potential plant diseases. So, grab your seed trays and get ready to embark on a successful gardening journey!

Other Seed Starting Posts You’ll Love:

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  • The Ultimate Seed Starting Guide
  • How to Make Paper Pots
  • DIY Soil Block Maker
  • Where to Buy Heirloom Seeds
  • How to Test Seeds for Viability and Germination