The Best Way to Clean & Disinfect Seed Starting Trays

Reusing seed trays can spread disease if not cleaned properly. Learn how to safely clean and disinfect them for healthy seedlings!

Close-up of a clean, empty seed starting tray with multiple planting cells, ready for use.

Every spring, I pull out my collection of seed trays, eager to get my garden started. But after years of gardening, I’ve learned the hard way that reusing trays without proper cleaning can lead to disaster—fungal infections, damping-off disease, and even mysterious seedling failures.

If you’ve ever lost a batch of seedlings to disease, you know how frustrating it can be. Reusing seed starting trays is a great way to save money and reduce plastic waste, but if they’re not properly cleaned and sanitized, they can harbor harmful pathogens that attack young plants. In this guide, I’ll walk you through the exact steps I take to safely clean and disinfect seed trays so they’re ready for healthy new seedlings.

Why You Need to Clean and Sanitize Seed Trays

It’s tempting to skip the cleaning process, but seed trays are a breeding ground for bacteria, fungi, and pests. Here’s why proper cleaning is essential:

Prevents seedling diseases – Damping-off, root rot, and fungal infections can linger in dirty trays.
Reduces pest issues – Leftover soil debris can harbor insect eggs and larvae.
Ensures healthy seedling growth – Clean trays promote strong root development without contamination.
Extends the life of your trays – Proper maintenance prevents buildup and cracking, so trays last longer.

Step-by-Step Guide to Cleaning and Sanitizing Seed Starting Trays

Keeping your seed trays clean isn’t just about aesthetics—it’s essential for preventing plant diseases and giving your seedlings the best start. Follow these simple steps to wash, disinfect, and store your trays properly so they’re safe to reuse season after season.

Step 1: Remove Any Debris

Before washing, get rid of leftover soil and plant material:

Dump out any remaining soil.
Use a stiff brush or old toothbrush to scrub away caked-on dirt.
Rinse the trays with a strong stream of water (a garden hose with a spray nozzle works great).

A used seed tray covered in soil, plant debris, and mold growth, showing the need for cleaning before reuse. — Dirty seed trays can harbor diseases like damping-off. Cleaning and disinfecting them prevents seedling loss.

Tip: If you start your seeds in peat pellets or soil blocks, trays will have less debris, making cleaning easier.

Step 2: Wash with Soapy Water

A thorough wash removes organic material that could shield pathogens from disinfectants.

Fill a large bin or sink with warm water and add a few drops of dish soap.
Submerge the trays and scrub all surfaces, paying close attention to corners and crevices.
Let them soak for 15–20 minutes before rinsing well with clean water.

A seed tray filled with old soil and leftover plant roots, showing why trays need to be cleaned between uses. — Leftover soil and roots in trays can carry diseases. Scrubbing and disinfecting trays keeps seedlings safe.

Step 3: Disinfect to Kill Pathogens

After washing, it’s time to kill lingering bacteria, fungi, and mold spores. Choose one of the following disinfecting solutions:

Option 1: Bleach Solution (Most Effective for Disease Prevention)

Mix one part household bleach with nine parts water (10% solution).
Soak trays for 10–15 minutes.
Rinse thoroughly with clean water.

Note: Bleach can degrade plastic over time, so use this method sparingly if you want your trays to last longer.

Option 2: Hydrogen Peroxide (Eco-Friendly Alternative)

Use 3% hydrogen peroxide (straight from the bottle) or dilute food-grade hydrogen peroxide (1 part peroxide to 5 parts water).
Spray or soak trays for 10 minutes, then rinse.

Option 3: Vinegar & Baking Soda (Gentle & Non-Toxic)

Fill a bin with one part white vinegar to three parts water.
Add ¼ cup of baking soda per gallon of water for extra scrubbing power.
Soak for 20–30 minutes, scrub if needed, then rinse.

Step 4: Dry Completely

Moisture breeds mold and bacteria, so drying is crucial:

Lay trays in direct sunlight to naturally disinfect and speed up drying.
If indoors, set trays on a drying rack or towel and allow at least 24 hours to fully dry before storing.

A close-up of a cleaned and dried seed tray with empty planting cells, prepared for seed starting. — After cleaning, let seed trays dry completely to prevent mold and bacteria from lingering.

Storing Clean Trays Properly

Once trays are disinfected and dry, store them in a way that prevents future contamination:

Stack neatly in a dry area – Avoid damp basements or garages where mold could develop.
Use a sealed bin or bag – This keeps dust, pests, and dirt out.
Label trays – If you use different trays for different plants, labeling prevents mix-ups next season.

My system: I store cleaned trays in a plastic tote with a few silica gel packets to absorb any lingering moisture. It keeps them fresh and ready for next season.

A seed tray with young green seedlings emerging from the soil, showing healthy plant growth. — Healthy seedlings thrive in clean trays. Avoid hidden pathogens by properly sanitizing your seed-starting equipment.

Troubleshooting & Tips for Reusing Seed Trays

Clean trays after every use to prevent disease buildup. If using multiple successions in a season, a quick rinse between plantings and a deep clean at the end of the season is a good practice.

It’s not recommended. Even if seedlings looked healthy, unseen bacteria and mold spores can remain in trays, leading to future issues. A simple vinegar or hydrogen peroxide rinse is an easy, eco-friendly way to disinfect.

Soap removes dirt and organic material but doesn’t kill pathogens. Pair it with a disinfectant (like bleach, hydrogen peroxide, or vinegar) for a complete clean.

Yes, but only for non-seedling purposes, like drip trays or shallow planters. Cracked trays harbor bacteria in crevices and can cause seedlings to dry out faster.

DIY Seed Tray Alternatives

If your seed trays are beyond saving, consider these budget-friendly alternatives:

Egg cartons – Perfect for starting small seeds but break down quickly.
Toilet paper rolls – Great for deep-rooted seedlings like squash.
Plastic clamshell containers – Like the ones from berries, they make mini greenhouses.

Save this pin so you never lose seedlings to disease again!

A clean black plastic seed tray next to fresh seedlings sprouting from soil, illustrating the importance of disinfecting seed trays before reuse.

Reusing seed trays is a smart and sustainable choice, but skipping the cleaning process can put your seedlings at risk. By following these simple cleaning and disinfecting steps, you can safely reuse trays year after year without worrying about disease.

Getting a jumpstart on your garden by starting seeds? Making sure your trays are clean is just one piece of the puzzle. You’ll also want to be sure you’re choosing seeds suited to your growing zone, testing older seeds for viability, and knowing when to start seeds indoors versus direct sowing. And if you’ve ever struggled with weak, spindly seedlings, there are easy ways to prevent legginess and grow strong, healthy plants right from the start.

How do you clean your seed trays? Have you ever had seedling losses from dirty trays? Share your experiences in the comments!