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How to Clean Seed-Starting Trays and Plant Pots: A Guide to Winterizing Your Garden Supplies

Forget spring cleaning—now is the time to get organized for next year.

If you live in an area that experiences all four seasons, you’ll need to winterize your garden at the end of the growing season. This typically looks like draining your irrigation systems, mulching your perennial plants, sowing cover crops, and removing dead and dying annuals from the garden.

One often overlooked fall chore is sanitizing seed trays and storing them for the winter. Even if you don’t get true winter in your area, fall is still a great time to clean and organize your spring seed-starting equipment so you’re more than ready for the next growing season.

Still not convinced? Keep reading for a list of reasons why garden cleanliness is next to godliness and what good garden hygiene will mean for next year’s seedlings.

Cleaning garden equipment is essential

Why bother cleaning seed trays and plant pots if they’re just going to get dirty again?

It might feel like unnecessary busy work, but cleaning seed-starting equipment serves more of a purpose than organization.

Easier to organize

It’s a no-brainer that we feel more at ease in organized spaces. Cleaning and organizing garden supplies and tools is a great way to close out one season and prepare for another successful year ahead.

Kills pathogens

Old soil can harbor pathogens that can lead to plant diseases, so sanitizing seed trays at the end of every growing season is important to minimize the risk of infecting next year’s crops.

Damping off, a fungal disease that can wipe out a tray of seedlings overnight is easily preventable by using clean seed-starting equipment and fresh potting soil. Root rot and bacterial wilt are other soilborne diseases that you want to avoid transferring from infected plants to healthy seedlings via dirty equipment.

Reduces plastic waste

Our durable seed trays are meant to be reused, reducing the amount of plastic waste that ends up in landfills. Chances are that you got into gardening to minimize your plastic footprint, and reusing seed trays and plant pots is a step in the right direction.

Saves money

The cost of garden supplies can really add up, so it’s wise to reuse what you can to save money in the long run. Invest in quality equipment from the beginning, and as long as you take care of your supplies, they will last for several seasons.

Opportunity to inventory supplies

This is also a great time to check seed trays for any signs of damage. Look for brittleness and cracking, and replace any broken trays with new ones.

The best time to order seed-starting supplies is in the fall since many of these products sell out when you need them by spring.

Equipment to clean

What should you clean? Anything and everything! Not to sound like a neat freak, but any equipment that comes into contact with plants and soil should be cleaned yearly.

  • Seedling flats
  • Bottom trays
  • Humidity domes
  • Heat mats (avoid getting soap or water on the electric cord)
  • Plant pots & reusable plant tags
  • Garden shears & pruners (be careful not to cut yourself when washing the blades, and pat dry if possible)
  • Landscape fabric (washing large pieces of plastic is annoying but necessary to prevent the spread of dangerous diseases between plants)

If you start your seeds in peat pellets, don’t try to wash and reuse them. Peat pellets are intended as single-use, biodegradable seedling pots that minimize transplant shock.

How to clean seed trays and pots

It’s as simple as cleaning anything else, really—and just as necessary for good garden hygiene. For the least mess and cleanup, be sure to perform this chore outside, although a deep utility sink would work just as well. Avoid getting chunks of bark and perlite in your drain if you can help it.

1. Gather your materials

Start by gathering all the necessary materials for cleaning. You’ll need a spray bottle, scrub brush, liquid soap, bleach, distilled white vinegar or hydrogen peroxide, and a water hose or sink.

Since this is an outside chore, plan to wash on a dry, sunny day so you’ll be comfortable, and your supplies will dry more quickly.

2. First rinse

Remove any leftover soil or plant debris from the trays by spraying the trays down with a water hose. Rinse both sides thoroughly, and don’t forget to check in between individual cells since dirt likes to hide out in cracks and crevices.

3. Soak

Soak the trays in a mixture of mild dish detergent and water for a few minutes to lift any stubborn dirt or stains.

4. Scrub

Add mild dish detergent to a scrub brush and gently scrub away. An old toothbrush is perfect for cleaning small and hard-to-get spaces.

5. Second rinse

Rinse thoroughly with clean water to remove any soap residue.

6. Sanitizing spray

Create a diluted bleach solution by mixing 4 teaspoons of bleach with water. Pour the mixture into a spray bottle and spritz the clean trays and pots to kill any remaining germs. Let the spray sit for a few minutes, and then wash any residue away with a quick rinse.

For a non-bleach alternative, add a spray nozzle to a bottle of 3% hydrogen peroxide solution and spray trays directly.

Distilled white vinegar is another all-natural disinfectant you can spray in this step. Although vinegar and hydrogen peroxide are effective cleaning agents when used in conjunction, don’t combine the chemicals in the same container, or a reaction may occur.

7. Air dry

Allow the trays and pots to air dry completely before placing them in storage.

Best practices for storing garden supplies

Once your seed trays and pots are clean, they can be safely stored until their next use.

Stack trays and pots

Seed trays and pots are made to nest together; the cleaner they are, the easier they are to pull apart. But there’s another, less frustrating way to store seed trays: instead of nesting seed trays, try stacking them bottom-to-bottom and top-to-top. This method of stacking (admittedly not the most space-efficient) reduces the risk of breaking trays since you won’t have to pull the trays apart.

Store away from direct sunlight

The worst thing you can do for plastic seed trays is store them in a greenhouse where they’re subjected to intense sunlight, which causes fading and breaks down the plastic faster. Store seed trays out of direct sunlight and out of the elements in a garden shed, closet, or basement. If you do store seed trays outside, cover them with a tarp to shelter them from the sun.

In conclusion

Winterizing a garden is no joke—and it comes with a laundry list of chores—so it never hurts to start on these chores a little early. Cleaning seed trays and plant pots is an important but often overlooked part of the process of “putting the garden to bed” for winter.

Even though it may feel like extra work, cleaning seed trays and pots is a chance to check for damaged or defective equipment and organize your garden supplies. Sanitizing seed trays also works to kill dangerous plant pathogens, and so long as you store seed trays in a protected area out of direct sunlight, you can reuse these products for seasons, saving you money in the long term.

And if you find that you need to replace some seed-starting equipment, now’s the time before our inventory sells out. Shop our full selection of seed-starting equipment today so that you have everything you need for spring! 

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