How to clean and disinfect your seedling trays

I know it feels cold and seems like spring is in the far distant future, but if you are starting your own seedlings in pots and trays from last year, you know it is time to start! An important step in preparing is to clean and disinfect your seedling trays.

Not cleaning them first can set your seedlings up for failure by exposing them to bacteria and fungus that can cause any number of issues from damping off to Botrytis.

dirty seedling trays

Step #1

Be sure to clean the underside of the trays and pots and scrape off any spider eggs or old nests that you find. Most often they look like white fluffy spots and stick to your fingers when you try to move them. Turn your trays upside down and remove as much loose soil and gunk as you can. Tip: rinsing them off when you put them away in late spring/early summer will make this task far easier.

Step #2: Wash!

Find a container large enough to wash your trays in and fill it half full with warm soapy water. They do not have to be totally submerged in water, just large enough to have maybe half at a time in the water. Of course, you could buy a Rubbermaid container large enough to fit the whole tray in at one time! Then you can let them soak and half the work is done for you!

Try to get this done on the warmest sunny day you can fit in your schedule. It is a real drag getting wet up to your elbows on a blustery cold day!
Cleaning and disinfecting your seedling trays is an important part of fall cleanup! Click To Tweet
Before we talk about the last step, a word about bleach as a disinfectant; it stinks. Bleach is a highly toxic and dangerous chemical.

  • Bleach causes respiratory problems and the fumes should never be inhaled.
  • Bleach can burn the skin and even cause major nervous system damage.
  • When combined with many other harsh chemical cleaners, new and dangerous chemicals are created that are bad for the environment and toxic to humans (and your pets too!).
  • Every year. about 1/4 of the calls made to Poison Control  for help are related to accidental ingestion of bleach or products containing bleach. Many of these accidents involve young children and can be potentially fatal.
  • Clorox Bleach Scores an F on the EWG Website due to its toxic ingredients

Below is a recipe for a home-made bleach alternative [1] if you do not want to use bleach.

Related  Ideal Temperatures for Seed Germination

DIY: All-natural Homemade Bleach Alternative


  • 3/4 cup 3% hydrogen peroxide
  • 1/4 cup lemon juice
  • 10-15 drops lemon essential oil
  • 3/4 cup baking soda
  • 7 cups water


Combine all ingredients in a container capable of holding 1/2 gallon or more. Shake well. This can be used as you would bleach.


Last step: and most important! Disinfect.

Add your bleach (or alternative) to the water and let your pots and/or trays soak for 10 to 20 minutes. Let them air dry and start fillin’ ’em up!

Let the growing begin!

The Ready Store
"The doctor of the future will give no medicine, but will interest his patient in the care of the human frame, in diet and in the cause and prevention of disease" ~ Thomas Jefferson

2 thoughts on “How to clean and disinfect your seedling trays”

  1. Hi. I had a package of seeds and they noted you should disinfect the seeds. They also suggested bleach which we will not use.

    Is this true and if so how do I disinfect seeds organically, do you know?

    • Hi Cheryl,
      This recommendation is likely based on fear of litigation. (I read that in a forum!) but I agree. I’ve never disinfected seeds. Even sprouting seeds, I rinse/soak them in a little bit of hydrogen peroxide, if that seems remotely close to necessary.


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