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How to Sanitize Seed Trays and Seed Starting Equipment

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An important first step in getting your garden ready for spring is to sanitize your seed trays. Read on for the simplest method of disinfecting your seed starting equipment to ensure healthy plants.

I have a confession to make.

I did not disinfect my seed trays and other seed starting equipment for the first five years or so of my gardening journey.

SoiEvery year, I would reuse the same seed trays, plastic pots, and other seed starting equipment like soil blockers and tools without batting an eyelash.

I would barely rinse off the equipment, let alone disinfect it.

And, I mostly got away with it, too!

That is until last year a few of my very young seedlings mysteriously began to shrivel up and die. It was like they were being zapped by some mysterious force from the bottom up.

I would learn later, this phenomenon is called “dampening off” and is a fairly common consequence of failing to disinfect your trays and other equipment each year before starting seeds.

This post is all about how to sanitize seed trays.

What is Dampening Off?

Dampening off occurs when pathogenic bacteria or fungus attack your young, vulnerable seedling, causing it to wither and die.

This failure to thrive can be mysterious, because the microscopic pathogens are invisible to the naked eye.

Basically, if you are reusing your seed starting equipment season to season (and we love a reduce, reuse, recycle moment!) there are probably microbes and pests lingering waiting for ideal conditions to multiple and wreak havoc.

The only way to hedge your bets against dampening off is to thorough clean and disinfect your seed starting equipment before reusing.

This process kills any pathogens leftover previous plantings before they have a chance to attack.

Another (Creepy) Reason to Sanitize

Beyond microscopic pathogens, there may be other hangers-on lurking that you’ll likely way to get rid of before starting your seeds.

One of my teachers, Jessica Robison, Founder of Acton Food Forest tells a harrowing tale of cleaning one of her seed trays and finding an active spiders nest.

This would have become a problem later when she brought her seed trays into her finished basement (where she does her seed starting) and the eggs hatched, causing a problematic spider infestation.

What to Disinfect

Disinfect any seed starting equipment you have used in the past.

Reused equipment has had exposure to microbial life that can be dangerous to seedlings.

Treat seedlings like human babies–they need special care!

Note: You probably do not need to new disinfect seed starting equipment that you’ve just purchased.

Seed Tray with Humidity Dome and Flood Tray

Soil Block Maker

How to Sanitize Seed Trays and Seed Starting Equipment

Cleaning vs. Disinfecting

The process of ridding your seed starting equipment of pathogens and pests consists of two basic steps:

  1. Clean
  2. Disinfect

What is the difference, right?

Well, cleaning technically refers to the act of washing off visible dirt and grime. This usually involves soap, water, and some friction.

In fact, the act of cleaning will usually remove a great deal of pathogens. You could probably stop here, but we want to be very conservative when it comes to the risk of dampening off.

Remember, dampening off could ruin a whole tray of seeds (if not more)!

That’s why we also need a disinfecting step.

Disinfecting refers to a chemical process that removes pathogens to an acceptable level, without killing ALL microbes entirely (that would be sanitizing, which despite the title of this article, we’re actually not achieving here.)

Disinfection Methods

There are several methods to disinfect your seed trays and seed starting equipment involving different chemical disinfectants.


Many people use bleach to disinfect their seed trays, but I personally think it’s a bit harsh and can’t stand the smell for too long.

Hydrogen Peroxide

Instead, I use hydrogen peroxide, which has no smell and safely breaks down into hydrogen and oxygen.

Commercially available 3% hydrogen peroxide is effective in removing the bacteria and fungi associated with dampening off.

Sanitizing Seed Trays – The Steps

Fill a container with warm soapy water. The size of the container will depend on the size and quantity of your seed starting equipment. I use a five-gallon bucket, but it could also be a larger tub. Some folks I know clean their seed starting equipment in a kiddie pool.

Clean your seeding starting equipment in the warm, soapy water using a sponge or brush. You want to remove visible dirt, grime, spiders’ webs, etc.

Rinse off your equipment. I use the outdoor hose for this step.

Apply 3% hydrogen peroxide to cleaned seed starting equipment. I like the hydrogen peroxide spray bottles for this step–super easy application!

Let the hydrogen peroxide sit for at least 20 minutes.

Wipe to dry.

Getting planting!

This post was all about how to sanitize seed trays.

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