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A small 6x8 foot household greenhouse is full of clean seed starting containers like small pots, trays, lids, and 6 packs. They're all lined up on the wood slatted shelves inside the greenhouse
All Things Garden,  Seed Starting

Sanitizing Seedling Containers & Garden Supplies

One excellent way to reduce waste in the garden is to reuse your seedling containers and nursery pots! This applies to ones you intentionally purchased for starting seeds, or any containers you bring plants home in from the local garden center – which you hope to keep and use again. If we are going to reuse these things, properly sanitizing supplies and tools between use or seasons is an important step to keep your plants healthy and disease-free! This article will go over a few non-toxic methods used to sanitize garden supplies.

On this homestead, we use a variety of plastic nursery pots, 6-packs, and 1020 trays with dome lids for starting seeds. The supplies we choose are high quality, heavy-duty, and durable. They’re ones that are meant to be reused year after year without easily cracking and breaking! We choose these over the single-use products like peat pellets, though that is just our personal preference. Even if you use peat pellets, you most likely have trays or cells that they sit in. Those should be cleaned too. For more information on seed starting tips and best practices, check out this post!

Why Sanitize Seed Starting Supplies?

While it may seem like just one more chore to do, and one that is easy to skip, sanitizing your garden tools and pots is something you should make an effort to do! Is sanitizing absolutely essential? Maybe not. Will all of your plants undoubtedly perish if you don’t do it? Probably not. On the other hand, starting the season with fresh clean supplies gives you a little extra (cheap!) insurance that your seedlings will be strong and healthy. It will also help eliminate that awful “what if…” or “I should have…” feeling if you do skip sanitizing, and something goes south.

When you are starting seeds and do not sanitize the seed containers, trays, and other pots between seasons, disease or fungal spores could be left behind and infect your new round of plants. This is especially a concern if you had any struggles with your seedlings the previous year. Or, if you are reusing containers from a garden center, potentially bringing in disease or pests that weren’t previously present in your garden.

One such disease that may inflict your new precious babes is called seedling blight, also known as damping off.

What is Damping Off?

Damping off is a somewhat generic term for when seedlings just up and die on you. They’re chugging along, looking all cute, perky and spry, and then Bam! Dead. Done. It is so tragic and frustrating to experience!

One of the most obvious signs and symptoms is when the seedling stem gets super thin and weak just above the soil line, and then flops over or wilts. What happened? Most likely a soil-borne disease or fungus is at fault. Sanitizing can help prevent this, along with using fresh sterile bagged seedling mix when you start seeds – not soil from your yard! Re-using old soil is another way to introduce pathogens to new seedlings.

A photo of a little cannabis seedling, toppled in half and dying. A portion of its stem is very very thin and almost hollow looking. This is damping off.
Damping off exemplified. See how thin and sad part of the stem got? There is no recovery form this. Photo courtesy of Marijuana Times

Other diseases

When you are out working in the garden, you should also take care to disinfect supplies –  such as your trimming shears. This should be done periodically as a good habit, but should most definitely be done whenever you are working around a plant with a known and obvious disease, to prevent it from spreading. For example, after a trimming a plant that has powdery mildew, sanitize your tools (and wash your hands!) before moving on to other plants.

How to Sanitize Seedling Containers, Trays, & Other Garden Tools

Before we get into the options of how to disinfect your supplies, I should note that it is important to try to start with fairly clean supplies at the beginning, before starting any of the methods below. I don’t mean clean clean. But at least lightly rinse or knock out any accumulated dirt before starting the disinfection process. The reason is this: the agent you use, be it vinegar or peroxide, will attempt to “clean” the dirt first, and use up a lot of its power and energy. So starting with less-than-filthy supplies will ensure your disinfectant is actually cleaning your pots and trays, not cleaning the dirt.

Option 1: Using Vinegar

One way to kill off any bad guys is to sanitize your supplies with plain white vinegar. Most household vinegar is 5% in strength. If you are working with a small collection of trays and pots, this could very easily be done with a spray bottle full of undiluted vinegar. Spray everything down well, and let the vinegar sit to do its thang. To be effective, vinegar needs at least 10 minutes of contact time on the item. 20 minutes is even better. After that, wipe or rinse them off. You may not have to rinse them, but because it’s so acidic, I do. I worry about the vinegar breaking down the plastic and making it more brittle.  

A hand is holding a spray bottle with "vinegar" written on it. In the background are various gardening supplies and tools, like nursery pots, 6-packs, a hand trowel, and a large bottle of plain white vinegar.
We reuse old cleaning bottles for vinegar spray, soap spray, or other homemade concoctions. Always clearly label your bottles!

We use this method to sanitize our garden shears, pots, or when working with a small number of seedling containers. I also spray down the interior walls of our greenhouse at least once a year. A spray bottle of vinegar is always readily accessible on this homestead! We actually use a homemade citrus and vinegar spray what we also clean our kitchen counters, sink, tub and shower with. Note: Due to its acidic nature, vinegar is not recommended for cleaning marble or granite countertops, and probably other types of sensitive stone. Do your homework before using it on yours! We just have crummy old laminate ones, for now.

What about soaking the supplies in vinegar instead of spraying?

Well, when I was researching the various methods for sanitizing garden supplies, many sources said to use undiluted vinegar, or at least somewhere around 75% vinegar to water. When too diluted, vinegar doesn’t have quite the same oomph to disinfect. That means that if you are working with a decent amount of containers to sanitize, you’d need a fairly large amount of vinegar to fill a tub, soak, and effectively sanitize your supplies. The same contact time as spraying applies here too. If you have fewer supplies to clean at once, soaking them could work just fine!

Option 2: Using Hydrogen Peroxide

Like vinegar, hydrogen peroxide is cheap, non-toxic, and effective at killing bacteria, viruses, mold, mildew, and fungus! Hydrogen peroxide is considered an environmentally-safe alternative to chlorine bleach. It breaks down into water and oxygen. Following the same steps as in option 1, fill a spray bottle with standard 3% household hydrogen peroxide (undiluted), spritz, and viola! Clean supplies. Also like vinegar, peroxide needs at least 10 minutes of contact time. Follow the same steps to wipe down or rinse off afterwards.

A hand holds a bottle of household hydrogen peroxide. In the background are a lot of green seedlings, inside a greenhouse.
Basic 3% household hydrogen peroxide is a safe, non-toxic bleach alternative!

If you are going to stick with a spraying method for either vinegar or peroxide and have a lot of supplies to sanitize, it may be easiest on your hands and most efficient to use use a pump pressure sprayer that can put out a constant stream. You know, opposed to a normal spray bottle that you have to repetitively squeeze.

Option 3: Make Your Own Non-toxic Bleach Alternative

Disclaimer: To be honest, I have been putting off writing and posting this because I have a feeling this section may raise a lot of eyebrows, and a lot questions. I contemplated omitting this part completely. But for the sake of transparency and “real life”, I figured I better just go ahead and share how we cleaned our seedling containers this year. For the record, I am not saying option three is better than two or one! It was just what happened to work for us. If you aren’t comfortable with playing mad scientist, stick to option 1 or 2.


Read this section carefully. Do not ever mix straight undiluted hydrogen peroxide with straight undiluted vinegar. Especially in an enclosed container, like a spray bottle! Mixing these two creates an acid. It’s not quite as scary as it sounds though. It is only dangerous and unstable if you create a strong, undiluted solution and store it mixed in an enclosed container. Or if you work with it in strong quantities indoors and inhale it. Hear me out here though! I did my research.

A photo of various garden supplies that are in need of a good cleaning. Pictured are dirty pots, 6-packs, and seedling trays. There is also a large plastic tub, waiting to be filling with cleaning solution to soak all the dirty supplies. A bottle of vinegar and hydrogen peroxide are shown, which should never be mixed undiluted in a closed container for safety concerns. I am going to mix them in water in an open container, to create peracetic acid - a non-toxic bleach alternative.
About to make some homemade Peracetic Acid

What is Peracetic Acid?

By combining vinegar and hydrogen peroxide, they react to form peracetic acid. Peracetic acid is a highly effective sanitizer that is widely regarded as very environmentally safe. It was first registered by the US EPA as a disinfectant in 1985. It is even more effective at killing microbes than bleach, and is used in place of bleach in the medical industry at times. Certain large chain grocery stories and restaurants use it as a sanitizer in their sink dispensers for cleaning dishes. Some cattle and beef industry facilities use it too! That’s pretty cool, if you ask me.

Yes it’s an acid, but so is vinegar. But you knew that though, right? Vinegars active ingredient, acetic acid, is actually a stronger acid than peracetic acid! If you correctly make a weak, diluted peracetic acid as I describe below, it is safe to work with.

If you google “Can you mix vinegar and hydrogen peroxide” the initial glaring answer you’ll come across is “NO!”. Again, that is mostly because of the concern of mixing it in an enclosed container. Warning bells also go off for some people when they see it makes peracetic acid. They’re like no, don’t create that stuff! Because at industrial strength, peracetic acid is highly corrosive, and a respiratory and skin irritant. It is made using industrial strength, highly-concentrated vinegar and similar hydrogen peroxide mixed together. While I appreciate people erring on the side of caution, that is not the household-level stuff we are talking about using here.

Why we choose to use paracetic acid to sanitize our seedling supplies:

The reason we even went down this path was sort of by accident, and also by necessity.  I certainly did not set out thinking, “Ooh, I wanna whip up a batch of homemade peracetic acid today!” It was more like: how can I get this task that I am not really looking forward to done as quickly as possible, with the supplies I have on hand? See, we had a TON of seedling containers to sanitize. We’re talking about one hundred 4” pots, several dozen 6-packs, and about a dozen trays and dome lids each. I absolutely did not feel like spreading them all out, spraying down each one on all sides, letting them sit, rinsing, and so forth. We also didn’t have nearly enough vinegar on hand in order to fill a large tub and soak everything at a high enough concentration to get the job done right.

I also really didn’t want to use bleach, so I started doing my homework. I saw options for peroxide, options for vinegar, options for bleach, and just one mention of mixing peroxide and vinegar to get a double-duty disinfectant. Unfortunately, that person didn’t include disclaimers about the hazards of mixing them undiluted, so I may reach out to them and bring that up. Reading their suggestion piqued my interest, but I definitely wanted to look more into this mixing business before doing it myself, since I know it’s very hazardous to mix some things – like vinegar and bleach for example.

Is Peracetic Acid Safe?

I scoured the scientific community and academic journals for answers. I also read a lot of forums where people bantered back and forth about whether it was okay or not, like this one. People had all sorts of differing opinions, but I decided to listen most to the people who chimed in with “scientist”, “university research director”, and “chemist” next to their name. Because you know what they say about opinions…  

This is the conclusion I came to: Household strength hydrogen peroxide (3%) and white vinegar (5%) can be used together safely (not mixed in an enclosed container!), especially if they are diluted and combined in sufficient water. The concentration of peracetic acid formed is so, so far below the industrial concentration that it will not be hazardous.  

How to Safely Mix Peracetic Acid to Sanitize Seed Starting Supplies

In a large clean plastic tub, about 15 gallons in size, I added just under two 5-gallon buckets full of water. They weren’t totally full because I had to carry and dump them, so it was probably about 7-8 gallons of water total. Then I poured in a full gallon of household white vinegar.  Next, I added one 32 oz bottle of hydrogen peroxide. All good. Then I repeated the process with a second tub. Following this recipe, you could scale down to use a 5-gallon bucket mostly full of water (at least ¾ full), add about half a gallon of vinegar, and 16 oz of peroxide.

Pictured are two large plastic tubs, about 12 and 15 gallons in size. Inside is a cleaning solution made of water, vinegar, and hydrogen peroxide. Seedling pots are soaking in the solution, getting sanitized. Some other supplies like 6-packs and trays are nearby, waiting to be cleaned next. This is all outside on a concrete sidewalk.
Round one soaking: the 4″ pots we’ve been able to use over and over for years! Next up, the 6-packs. Then the trays and domes will get their bath last!

Next, I added as many pots or trays that would fit in and stay submerged. After they soaked for 15 to 20 minutes, I pulled them out and put the next batch in. Using a 5 gallon bucket nearby, I quickly dunked the now-sanitized pots and 6-packs into the bucket of clean water, to give them a rinse. For the larger trays, we gave them a quick spray with the hose. Then all the clean supplies went into the greenhouse to dry. For the extra dirty trays, I scrubbed them with a brush too. I had to do about 3 batches to get through everything while still giving them all adequate contact time. But it was way less of an effort than the other options, in my opinion!

Yep, I put my hands all up in it. Not a single tingle. It was fine. And I have fairly sensitive skin. Not that I would have done this job inside, regardless of what we were working with (too messy!)… but for the record, I did it all outside, so adequate ventilation was not a concern.  Though I don’t really think it mattered. It didn’t smell like anything. Just a slight vinegar odor. From what I read, industrial strength peracetic acid is extremely strong and noxious. Like, it burns when you inhale it.

Shown is two large plastic tubs, about 12 and 15 gallons in size. Inside is a cleaning solution made of water, vinegar, and hydrogen peroxide. There are seedling trays inside the cleaning solution, and a hand holds a scrub brush up over the trays.
Dang! Look how dirty that cleaning solution was towards the end. We chose to start with the pots and 6-packs first, while the peracetic acid was still at its strongest, because those supplies are in most direct contact with the soil and seedling. The trays and dome lids were less of a priority, so they got the less fresh sanitizing solution.

If it’s “so weak”, is it still even effective for sanitizing?

I think so. And in this case, it was better than the alternative – either a very tedious task of spraying the supplies, using bleach, using uber-dilute peroxide or uber-dilute vinegar on their own, or not sanitizing at all! While I was scrubbing the trays, they bubbled a bit like peroxide does when it is working. I took that as a good sign!

After all was said and done, I came across this quote by a food scientist at Virginia Polytech that made me feel even more assured that my little science experiment went pretty well:

“If the acetic acid [vinegar] got rid of 100 organisms, the hydrogen peroxide would get rid of 10,000, and the two together would get rid of 100,000 organisms.”

Susan Sumner, Science News Online

So even though my vinegar was pretty dilute, and my hydrogen peroxide was pretty dilute too, their combined power is pretty dang strong!

Disposing of vinegar or peracetic acid

If you used the soaking method using vinegar or peracetic acid and have a good amount to dispose of, do not dump it in your garden where plants you care about are growing. Acids, such as vinegar, are often used as a natural weed killer. They’re environmentally “non toxic” because they break down quickly and have no lasting harm, but that doesn’t mean you want to water your favorite plants with it. Go ahead and give it to the weeds, if you want! We dumped our tubs in a mulched corner where no plants were growing.

So there you have it. You probably think I am nuts.
I am okay with that.

I hope at least one of these non-toxic methods to sanitize garden and seedling supplies will work for you! Cheers, to disease-free seedlings.

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  • Amy B

    Hello, so the first thing I thought of is how this may be a problem in MN. What I mean is there, I can see organisms or bacteria suriving in dirty pots because the weather is warmer all season. I only use soapy water, sun dry the pots and store out in the greenhouse until next season. Do you think anything survives our below zero temps that sometimes go for a few months? I always lay everything out in the hots sun all day until dry, thinking that helps? So what do you think, thanks!!!!! Love the info.

    • Aaron (Mr. DeannaCat)

      Hi Amy, we don’t always have the time to thoroughly sanitize our pots although it is considered best practice. Washing them with soapy water as you do seems like it is working so I would just stick to that for now. Hope that helps and have fun growing!

  • Heather

    Hi! Thanks for such an informative, detailed article! I’m curious if you would recommend sanitizing brand new, out of the box seedling containers, or only after you’ve used them before? Do you just sanitize new ones even for good measure?

    • Aaron (Mr. DeannaCat)

      Hello Heather, we don’t sanitize new containers. We are only worried about potential plant diseases that may be left over from the previous season or use. Good luck!

  • Melissa Barreto

    I was wondering if you knew if the peracetic acid would work to kill viruses too? My garden got hit by mosaic virus and I just cant seem to figure out what I need to do in order to sanitize against that virus. Thanks!

    • Aaron (Mr. DeannaCat)

      Hello Melissa, I’m sorry you’re having a difficult time dealing with this difficult garden virus. Unfortunately there is no cure for Mosaic virus, the only hope is to prevent and control it. You need to remove all the plants and plant material that has been infected by it and place it in the trash, do not compost this material as it will stay around. Going forward, look for plants that are more resistant to Mosaic virus, Johnny’s seeds does a good job of listing what diseases their different varieties of vegetables are resistant against. Also, it is said that insects help spread the virus so it may be a good idea to invest in hoops and row covers to make it more difficult for the insects to move about your garden. We have an article on that if you want to check it out: Using Hoops and Row Covers for Garden Pest Control, Shade & Frost Protection. Thanks for reading and good luck!

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