Do you ever get frustrated with past years’ seed trays and pots? They always seem to overflow their storage space, and never fail to harbor ant colonies, spiderwebs, and all kinds of insects. Old seed trays always end up stuck together or crack in the sun. You hate buying new plastic every year, but you’re fed up with recycling old seed trays.

What if there was a way to reuse seed trays and safely store them without all that frustration?

Sanitizing seed trays is so simple that there’s no excuse not to. Save space in your greenhouse and money in your wallet by cleaning your seed trays out once a season. By doing so, you’ll kill off fungal spores that cause damping off, giving your seedlings the best possible start.

Reasons to reuse seedling trays and pots

Throwing away used trays and pots is certainly easier, but since when have you been interested in taking shortcuts? Here are a couple of reasons why reusing seed trays is worthwhile work.

Less waste

We all understand how horrible single-use plastics are for the environment. So the next time you’re frustrated with your seed trays, think twice before throwing them in the garbage. 

Obviously, you can’t use seed trays that are broken. And it’s a pain when worn-out seed trays are too warped to stack together properly. That’s understandable to retire those trays. But the new pots that you bought last season? Clean them up and they’ll be good as new!

Save money and space

Seed trays aren’t all that expensive, but that’s still money that could be used to buy new seeds or potting soil, or funds that could be put towards a shiny new piece of equipment for your garden! 

You can’t pretend that space isn’t an issue–the more trays you accumulate, the more space they take up in your garage or seed-starting room. So, only keep what you need, and keep the stack clean and tidy so you won’t become stressed or tempted to buy shiny new seed trays.

Are sanitizing seed trays necessary? 

There are a few topics that divide gardeners: till or no-till, use of organic or conventional fertilizers, and whether to water in the morning or the evening, to name a few.

There are some gardeners, like Charles Dowding, who argue that sanitizing seed trays isn’t really necessary to prevent damping off. In this article from the Sunday Times, Jane Powers analyzes Dowding’s book, Gardening Myths and Misconceptions: 

Damping-off (a fungal disease of seedlings) occurs in humid conditions when the infant leaves are too close, watered too often or sown too early. “I have successfully reused module trays more than 100 times, without any cleaning at all,” Dowding says.¹

Dowding and Powers do have a point. Damping off is a soil-borne fungal disease that is often transmitted via reusing unsterilized seed trays from season to season. But sanitizing seed trays doesn’t totally eliminate the chance of your seedlings damping off, as user error is just as often the culprit as dirty equipment.

There’s no harm in sanitizing seed trays against this soil-borne illness. Yes–for those gardeners who have essentially eradicated damping off from their seed-starting areas and those who have access to healthy, sterile compost, sanitizing seed trays may not be needed, but for the average gardener, it just makes sense.

Damping off is the stuff of gardeners’ nightmares. What a disappointment to invest so much time, energy, and love into your seedlings, only to watch them fold over and die overnight? For me, the extra work of sterilizing seed trays as a preventative measure is totally worth it. 

Luckily, taking preventative measures against damping off is as simple as thoroughly washing your seed trays out once a year. Of course, damping off may still develop in sterile seed trays if you’re watering improperly–so be sure to read this article to familiarize yourself with the warning signs of damping off.

Sanitizing your seed trays isn’t the sole underlying problem that results in seedlings damping off, but starting with clean seed trays will provide your seedlings with the best opportunity to never have to battle that sinister fungal disease. 

How to sanitize seedling trays and pots

While it does feel like a chore–here’s yet another thing to wash – I recommend that you pick a day at the end of the growing season, or at the beginning of the new season, to tackle your used seed trays. Of course, you can break this task up into smaller batches on a few different days, or you could knock it out all at once. It comes down to personal preference.


Have all these things on hand before you start:

  • Waterhose with a nozzle
  • Bucket, tub, or trough
  • Spray bottle
  • Scrub brush, toothbrush, or sponge
  • Dish detergent
  • Bleach
  • Optional: hydrogen peroxide
  • Optional: apple cider vinegar


Feel free to get creative with this process–these are just guidelines. 

  1. First rinse

First, you’ll need to rinse your seed trays and pots to wash away excess soil, bugs, etc. I recommend doing at least the first rinse outside, so you won’t be struggling to wash pieces of perlite or pine bark down the drain. Lay your trays out on a picnic table or on the grass and hit them with the water hose, on the jet setting, for a solid rinse. 

  1. Scrub

Now it’s time to get dirty. Put on a pair of rubber gloves, take up your favorite cleaning utensil, and get after it! You can mix up a soapy solution with warm water in a bucket and dunk your sponge or scrub brush in it occasionally, or you can put a drop of detergent in the container and scrub thoroughly. 

Use a toothbrush to get those hard-to-reach places in seed trays that have individual cells. You’ll be fine using a scrub brush or a sponge on open bottom trays and humidity domes. Don’t forget to lightly go over your heat mats as well–but make sure the heat mats are unplugged first. If you can help it, don’t get any water or soap on the thermostat. 

It may take a little elbow grease to get all the grime off your seed trays and pots, but don’t force it so much that you bend or break the plastic. You can always leave the worst ones to soak while you clean the others. 

  1. Second rinse/dunk

Next, rinse the soap off the trays. You can either hit them with the water hose again, or you might opt to dunk the trays in a tub to conserve water. If you do go this route, remember to start filling the tub several minutes before you expect to be using it to save time. A children’s swimming pool, if you have one on hand, is perfect for this step. 

Alternatively, use the water hose to rinse the seed trays again. Either way, don’t let any soap dry on the plastic, as it’ll be harder to wash away. 

  1. Spray with sanitizing bleach solution

While the seed trays are still wet, you’ll want to spritz them with a powerful cleaning agent to make sure to kill off all those nasty fungal spores.

If you use bleach, you can make a diluted bleach solution in another container without issue. Dedicate that spray bottle to bleach cleaning solutions, and be sure to label it with a marker. Put on some gloves and mix one part bleach to nine parts water for an effective and safe bleach sanitizing solution. 

Be sure to spray the seed trays and pots thoroughly–you want to spray to be dripping through the holes in the bottom. Allow the spray to sit on the trays for at least 10 minutes before rinsing.

  1. Rinse again

Dunk your seed trays in the tub for another good rinse or hit them with the water hose one last time. 

  1. Air dry

Finally, you’re done! Well, almost. You still have to stack your seed trays and transfer them back to storage in your greenhouse or seed starting room, but for now, you can rest. Allow the seed trays and pots to fully dry before you attempt to stack them together–otherwise, the pieces of plastic will just stick together. Save yourself the frustration and have a little patience.

Other options

If you’re not all that excited about using harsh chemicals to sanitize your seed trays – that’s totally understandable! Here are some easy, all-natural substitutes.

Bleach-free sanitizing spray

For a bleach-free alternative, try substituting hydrogen peroxide. Take care to not mix bleach and hydrogen peroxide together, as a chemical reaction will take place. Instead, choose one or the other. 

Use a 3% hydrogen peroxide solution available at most stores or pharmacies. Buy a spray nozzle that fits the bottle rather than transferring the solution to another spray bottle–hydrogen peroxide is stored in opaque containers because light breaks down the molecules to regular water.

Organic/all-natural detergent

Try using a certified organic soap, like Mrs. Meyers dish soap or Dr. Bronner’s Castile soap to scrub out your seed trays.

For an all-natural sanitizing spray, use Bragg’s Organic Apple Cider Vinegar. Mix up to one cup apple cider vinegar with two cups of water to make an all-purpose cleaner and sanitizing spray. 

Getting the maximum life out of your seed trays

Now that you’ve worked so hard to clean up your old seed trays, you probably want to know how to keep these pieces of flimsy plastic functional for years to come. Cleaning is only one part of the equation–the other trick to keeping seed trays nice is to store them properly. 

Protect from sunlight

Sunlight will break down plastics faster than anything else. Store your seed trays in a dark place, if possible, like a garage or a shed. Don’t store your extra seed trays in a greenhouse unless they are underneath the tables or covered with a shade cloth or tarp. 

Stack upside down

You may have noticed that your seed trays tend to stick together when you sit them one inside of another. And how many of us, in exasperation, have ripped plastic seed trays trying to pull them apart?

Try stacking seed trays the opposite way– stack the trays top to top and bottom to bottom, so that they never collapse in on each other. This technique doesn’t save space, but it certainly saves time and frustration. 

Invest in quality seed trays

If you’re serious about producing less waste and giving your plants the best possible start, it might just be worth investing in some quality seed trays. These are a couple of my favorites:

Produced by Neversink Farm, Winstrip Trays are an investment but they will revolutionalize your seed-starting technique. These plastic trays are sturdy, and while they are divided into cells, the bottom of the cells are open. This open design air-prunes seedlings before they become rootbound and is meant to mimic soil blocking. 

Bootstrap Farmer has an extensive online store that has affordable seed starting trays to meet every need. Trays are sized from 32-count pots and inserts to 200-cell trays. Bottom trays, humidity domes, and other seed-starting equipment is also available for purchase. 


Reusing seed trays and pots is a fantastic way to reduce plastic waste while saving yourself time and money. Whether or not you choose to sanitize your seed trays, reusing those plastics is a worthwhile garden chore. You might even find it therapeutic, like washing dishes or folding laundry! Treat yourself to quality seed-starting equipment, and if you take care of it properly, you’ll get good use out of these tools for seasons to come.  


¹ Powers, Jane “Ok, you can stop washing those pots,” The Sunday Times 19 October 2014 pp. 1-2,

Similar Posts

Leave a Reply

Your email address will not be published. Required fields are marked *