Disinfecting Seed Flats and Trays

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Disinfecting Seed Flats And Trays

Have you ever had an entire flat of seedlings shrivel up and die on you? This is one of the biggest frustrations I hear people talk about when they are new to starting seeds indoors. There is nothing more frustrating than spending all that time starting your seeds, then getting super excited when they sprout and babying them for weeks… only to watch the entire flat of seedlings shrivel up and die. Ugh, it’s not pretty!

Related Post: DIY Seed Starting Mix

Why Are My Seedlings Dying?

The reason seedlings shrivel up and die off at the base is because they suffered from a common problem called damping off (also known as seedling blight). Seedling blight is a fungus that attacks and kills seedlings, and it is easily preventable.

Seed Flats Trays

Seed Flats Trays

How To Prevent Seedling Blight

When starting seeds indoors, it’s essential that you disinfect the seed flats, trays and covers before you use them. It’s fine to use brand new seed starting flats and trays out of the box, but dirty indoor seed starting equipment should be disinfected every time you reuse it. This is the easiest way to prevent seedling blight, and will save you tons of time (and heartache) in the long run.

Related Post: How To Clean Winter Sowing Containers

Soak Flat Trays

Soak Flat Trays

How To Disinfect Indoor Seed Starting Equipment

Supplies Needed:

  • A bucket or large plastic bin
  • Paper towels or a small cleaning brush
  • Bleach
  • Dish soap (optional)


  1. Wipe the loose dirt out of the flats and trays using a paper towel or small cleaning brush.
  2. If there’s any dirt that is hardened on, wash the flats and trays in warm soapy water.
  3. Disinfect seed flats and trays in a bucket (or plastic bin) of a water and bleach mix for 15-20 min. I recommend using a solution of 1 part bleach to 9 parts water.
  4. Give them a quick rinse and let them air dry, now they are ready to use for starting seeds.

Related Post: Tips For Starting Seeds Indoors.

Seedlings Growing In Flats

Seedlings Growing In Flats

Ok, ok – I know what you’re thinking. Yes, it will take you a little extra time to disinfect your seed flats and trays, but the effort is well worth it to ensure your seedlings have a healthy start. Trust me, it’s not worth the risk to try to save yourself a little extra time.

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For more help with seedlings and seedling care, click here… Seedlings

Share your stories about dealing with seedling blight in the comments section below.



  1. says

    Maybe I'm lucky, but I've never had a damping off problem, and I never wash my dirty pots — I definitely never use bleach solution on them (too much work). I'm certain I'd start doing this as soon as I had some losses due to damping off though.

  2. says

    Hi Tessa, Thanks for your comment! You'll have to tell me more about the chamomile tea. I'm guessing it might kill the bacteria that causes damping off? I will look that up, thanks for the tip.

    Hi Alan – yes, you have been lucky! I also reused my flats for a few years without any problems…then one year lost almost all of my seedlings at once. It was devastating! Hard lesson

  3. Beth says

    Thanks for this tip. I was going to reuse some trays this year and never even thought of cleaning them. Any thing else I need to watch out for?

  4. Heather says

    If you do the disinfecting in your bathtub you can clean all your trays at once. And bonus, scrub down your tub after for a disinfected tub :-) Rinse well afterward, obviously.

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