How to Clean Seed Starting Trays

Seed starting trays, or seed starting containers, are plastic trays with multiple small compartments for soil and seeds. Many seed starting trays come with a clear plastic dome to create a miniature greenhouse. These trays offer an easy, compact growing environment for most garden seeds.

You’ll find that once you invest in them, you’ll want to use them year after year. And that’s when problems start. If you don’t disinfect or clean them properly, you may accidentally transmit diseases to your newly emerging seeds and kill off your new plants.

Here’s how to clean seed starting trays each year to prevent diseases among your seedlings.

Disinfect Trays to Prevent Damping Off

Reusing seed starting trays without disinfecting them can cause several diseases. Damping-off fungus, rot, mold and other microorganisms thrive in the warm, moist environment that many seeds need to germinate. You can prevent these problems by disinfecting equipment prior to using it each year.

Put Trays Away CLEAN

The first step is to always put away all seed starting equipment at the end of the season clean. Use your garden hose with the setting on high or a strong spray to rinse trays. Let them dry in the sun. Then store them in your shed or garage until next year.

How to Clean Trays for Seed Starting

To sterilize your seed starting trays and equipment, you will need:

• 9 cups of water
• 1 cup of household bleach
• 1 large bucket or a stopper for a big sink to submerge the trays

The ratio of bleach-to-water to disinfect gardening equipment is always 9 parts of water to 1 part bleach.

You can adjust the amounts listed above by whatever you need them to be, as long as the proportion of bleach to water is kept the same.

Make sure that all loose soil is removed from seed starting trays. Work in a well-ventilated area. Mix the water and bleach in a large bucket. Submerge the trays into the water and bleach solution. You may wish to wear rubber gloves to protect your hands.

Let the trays soak in the bleach and water solution for 10 to 20 minutes. Then remove them from the solution, rinse with cool water, and let them air dry.

The trays are now disinfected and ready for use. If you don’t use them right away, there is no need to disinfect them again before use. Rinse off any dust that has accumulated on them and they are ready to use.

Pro Tip: Always Use Sterile Seed Starting Soil

Another pro trick to prevent diseases in seedlings is to always use sterile, bagged seed starting mix from the local home and garden center rather than garden soil from your backyard. You may also use bagged potting soil, such as the kind sold to replant house plants.

Why do professionals and master gardeners choose sterile seed starting soil instead of simply digging up soil from the yard?

Soil from the yard contains bacteria, mold spores, fungi, insects, and insect eggs. In your nice warm home, with a comfy moist environment, all of those will grow and thrive…and that’s NOT what you want germinating in your seed trays. No one wants to find their plants swarming with newly hatched spiders, flies, or beetles!

Using Peat Pots Instead of Soil to Start Seeds

Another easy way to prevent disease is to use peat pots or disks. These may be purchased from your local home and garden center, plant nursery, or online stores.

To use peat pots, remove them from any plastic or netted wrappers and submerge in cool water for 10 minutes. The peat expands into a unique mini pot. Place the expanded peat pots into a tray. Each pot has a small hole or depression in the top. That is where you insert the seed.

After planting one seed in each pot, water the peat pots daily. When you are ready to transplant seedlings into the garden, slip the whole pot, peat and all, into the soil. It’s a great way of starting seeds, especially for plants who hate to have their roots disturbed, because you never have to tug or pull at the plant or its roots.

My Job as a Kid: Peat Pot Duty

My dad loved to garden, and I loved tagging along after him no matter what he was doing. Each spring, he’d pull out his pots and trays and plant seeds. We had a heavy soapstone sink in the basement next to the washing machine. He’d put the lid down on the machine and spread out his seed starting equipment. Then, he’d hand me the peat pots. It was my turn to help.

I remember watching with excitement as the disks expanded in the cold water in the sink. It was like magic! I’d plunge my hands into the icy water just to feel the rough and slippery peat disks. Sometimes, I could hear them crackle slightly as the dried peat moss absorbed water like a sponge. I’d fish them out and hand them proudly to my dad so he could start his tomatoes and peppers.

Every time I smell peat moss or see packets of peat pot disks at the garden center, I smile, and wish my dad was still here so we could plant seeds together.

Need More Help Starting Seeds? Check Out These Articles

I’ve written many other articles on starting seeds. Please visit the links, below, for more information on starting seeds.

• Choosing Garden Seeds
• Are Organic Seeds Better?
• Best Light for Starting Seeds
• How to Start Seeds
• Seed Inventory

First published January 2016. Updated May 20, 2021 to add more information and improve readability.