How to Clean and Sanitize Seed Trays Safely: Bleach, Vinegar and Heat
How do you clean and sanitize seed trays? Clean seed and microgreen trays in four steps: remove roots, seeds and growing medium; wash the tray with warm water and mild soap; sanitize it with a product suitable for hard plastic, following the label (the University of Wisconsin-Madison recommends 1 part disinfecting bleach to 9 parts water for 30 minutes, then a thorough rinse); then rinse as the label requires and let it dry completely. Do this after every harvest.
The order matters more than the product. A sanitizer works on a clean surface, so washing always comes first, and no sanitizer makes up for roots and medium left in the corners. Following this order lets you reuse the same growing trays crop after crop.
Table of Contents
1. Why you need to clean trays after every harvest
Leftover soil, roots, old seeds and water stay on a used tray even when it looks empty. Mold, bacteria and fungi from the previous crop survive in these residues and can attack the next one, for example causing seedlings to collapse at the base (damping-off). This is why university extension services recommend washing and disinfecting previously used flats, trays and pots before sowing again.
Microgreen trays are reused crop after crop, often with only days between harvest and the next sowing, so the residues of one crop meet the next one quickly. Iowa State University recommends that previously used flats, trays and pots are cleaned and disinfected before use, and the University of Wisconsin-Madison gives a soaking procedure for reused containers as one of its tips against damping-off.
Clean trays are only part of prevention. The University of Wisconsin-Madison also recommends buying high quality seed from a reputable source and not overwatering, because the organisms that cause damping-off are more active in wet soil. Bottom watering in a pair of trays makes it easier to control how much water the medium takes up. See our microgreen seeds.
2. Cleaning, sanitizing and sterilizing: what is the difference?
This guide describes washing and disinfecting trays before reuse, the procedure that many people search for as "how to sterilize seed trays". It does not make trays sterile.
- Cleaning removes visible dirt: soil, roots and seeds. It is always the first step.
- Sanitizing or disinfecting reduces the microorganisms that remain on a surface that looks clean, with a product used as its label describes. It works properly only on a washed surface.
- Sterilizing in the strict sense means making a surface sterile, which this home procedure does not promise. Many guides use the word loosely for washing and disinfecting.
In practice, skipping either step does not work. Washing alone leaves microorganisms on the surface, and a sanitizer cannot reach the plastic under a layer of dirt and roots.
3. How to clean and sanitize trays step by step
- Remove debris. Empty the tray and remove roots, seeds and growing medium with a brush, sponge or paper towel. Pay attention to the corners and, in multi-cell trays, to each cell. Do it straight after harvest: dried roots stick to the plastic and take much longer to remove.
- Wash. Scrub the tray inside and out with warm water and mild soap or washing-up liquid. Soak heavily soiled trays first to loosen dried dirt. Rinse off the soap before the next step.
- Sanitize. Use a product suitable for hard plastic surfaces and, where required, for food-contact equipment. Follow the label for dilution, contact time, rinsing and protective equipment, and keep the surface wet for the whole contact time.
- Rinse and dry. Rinse off any residue when the product instructions require it, then let the trays drain and air-dry completely on a clean surface or rack before stacking them or sowing again. Trays stacked wet stay damp between the walls for a long time.
Cleaning drainage holes
Roots grow into drainage holes and residues collect around them, so trays with many holes need extra care. Soak the tray first, push out roots with a small brush, then rinse each row of holes under running water before sanitizing. To check that the holes are open, hold the tray against the light. Blocked holes do more than look untidy: water cannot rise evenly into the medium during bottom watering, and parts of the next crop stay dry.
In multi-cell trays, treat every cell as a small tray: empty it completely, brush the bottom and the corners, and only then put the whole tray into the sanitizer.
4. Can you reuse seed and microgreen trays?
Yes. Reusing trays is one of the simplest ways to cut the running cost of growing microgreens, and it means less plastic to throw away. Trays made for repeated use, including all our growing trays, can be reused many times, as long as you clean and sanitize them after every harvest and they are not damaged. Replace a tray when it is:
- cracked or broken, including fine cracks around the holes;
- deeply scratched, because scratches hold dirt and are hard to sanitize;
- deformed, so it no longer fits its matching tray or lies flat;
- covered with deposits you cannot remove.
For frequent handling, our "10x20" Extra Strength Growing Tray is made of recycled PE and is more flexible than the standard version, and the "10x20" Shallow Growing Tray is also made for repeated use. Compare all models in our growing trays category or in our guide Microgreen tray sizes compared.
[product id="112, 146"]
Between crops, store clean, dry trays where they stay clean, away from used trays and growing medium. For new pots and flats, the University of Wisconsin-Madison advises keeping them in sealed plastic bags until use, to prevent contamination.
5. What to use to sanitize trays
Use a sanitizer suitable for hard plastic and follow its label; the bleach procedure below is the one described by university extension services. Use one product at a time and never mix products. Three types of products are used for plastic trays:
Bleach
The University of Wisconsin-Madison advises soaking reused containers in 10% bleach (1 part disinfecting bleach, 9 parts water) for 30 minutes and then rinsing well to remove bleach residues; Iowa State University recommends the same 1:9 solution after washing in soapy water. Bleach concentration differs between products, so check that yours is a regular disinfecting bleach and follow its label.
For many trays, two tubs make the work easier: one with soapy water for washing, one with the bleach solution for soaking. Submerge the trays completely, so the solution reaches the holes and the underside, and rinse them thoroughly in clean water at the end.
Bleach safety
- Wear gloves and work in a well-ventilated place or outdoors, and follow the protective measures on the product label.
- Never mix bleach with vinegar, acids, ammonia or other cleaners. According to the UK Health and Safety Executive, chlorine-based disinfectants release toxic chlorine gas in contact with acid.
- Keep the surface wet for the whole contact time and rinse the trays thoroughly afterwards. Replace and dispose of the solution as its label says.
Vinegar
White vinegar helps remove mineral deposits from trays, but it does not kill all germs. Use it for cleaning, not as a disinfectant, and never in the same bath as bleach. If you use it, rinse the trays well before you sanitize them.
Boiling water, hot water and the dishwasher
Do not immerse plastic trays in boiling water and do not wash them at high temperature unless the manufacturer confirms that the material withstands it: hot water can deform plastic trays, and a deformed tray may no longer fit its matching tray. For bottom watering this matters, because the tray with holes must sit evenly in the tray without holes. Heat resistance is not stated for our tray models, so we do not recommend boiling water or a hot dishwasher cycle. Warm water, soap and a compatible sanitizer are the safer option.
Hydrogen peroxide
Hydrogen peroxide products can be used to sanitize trays if the label allows it for hard surfaces. Follow the label for concentration and contact time, wear gloves and do not mix them with other chemicals.
6. Cleaning trays in bulk: soaking tubs and tray washers
A microgreen tray washer is a machine for washing many trays at once; without one, you can clean many trays by hand in batches. If you grow commercially, organise cleaning like this:
- Collect used trays after harvest and remove roots and medium straight away, before they dry.
- Soak the trays in a large tub of warm water with detergent, scrub them one by one and rinse off the detergent.
- Sanitize them in a second tub with a prepared solution, observing the contact time, and rinse them if the label requires it (always after the bleach procedure above).
- Rinse and dry the trays upright on a rack, so water drains from the holes.
Working in batches keeps clean and dirty trays apart and gives each tray the same treatment. Plan for enough trays for one batch to dry fully while the next is in use.
If you consider a tray washer, check three things before you buy: the largest tray size it accepts against the real dimensions of your trays (our growing trays are up to 59.5 cm long and up to 36.5 cm wide, depending on the model; check the outer height of your model as well), whether it only washes or also disinfects, as confirmed by its manufacturer, and how many trays it handles per hour compared with your workload. If it only washes, sanitize the trays afterwards.
7. How often to clean trays
Clean and sanitize trays after every harvest. If you have had mold or damping-off, be especially thorough, and include the trays used as blackout covers and the lower trays used for bottom watering: they touch the same water and the same crop.
After harvest, remove the used mat or growing medium together with the roots before you wash the tray, and do not leave residues in the corners or holes. For the next crop, prepare a CocoMat or other growing medium as described on its product page.
- a stiff brush for corners and a small brush for drainage holes;
- a sponge or cloth;
- a tub or bucket for soaking and a second one for sanitizing;
- protective gloves;
- a drying rack or a clean surface where trays can stand upright.
Keep these tools only for trays and clean them as well: a brush that goes from a tray with mold to a clean one can carry the problem with it.
FAQ
Can I reuse microgreen trays?
Yes, if they are not cracked, deeply scratched or deformed and you clean and sanitize them after every harvest.
What is the best way to sanitize seed trays?
Wash them first, then sanitize them with a product suitable for hard plastic, following its label. The University of Wisconsin-Madison recommends soaking in 1 part disinfecting bleach to 9 parts water for 30 minutes and rinsing well.
Can I put microgreen trays in the dishwasher?
Only if the manufacturer confirms that the tray material withstands the temperature. Hot water can deform plastic trays; warm water and mild soap are the safe choice.
Is vinegar enough to disinfect trays?
No. Vinegar removes mineral deposits, but it does not kill all germs. Use a sanitizer suitable for hard plastic and follow its label.
Can I mix bleach and vinegar?
No. Mixing chlorine bleach with acids such as vinegar releases toxic chlorine gas.
Do I need a microgreen tray washer?
It depends on how many trays you wash and how much time it takes. You can clean trays by hand with a tub, a brush and a sanitizer; a washer is worth comparing when washing takes a large part of your working time, by looking at its price, its capacity and the tray sizes it accepts.
How do I clean many trays at once?
Soak them in a large tub, scrub with a brush and rinse, sanitize them in a second tub, rinse as the label requires and dry them upright on a rack.
Summary
Remove debris, wash, sanitize and dry: these four steps after every harvest reduce the risk of mold and disease passing to the next crop. Use a sanitizer that suits plastic, follow the label, never mix chemicals and avoid boiling water. Replace trays that are cracked or deformed. Trays, mats and other accessories are in our supplies for growing microgreens.
Sources and Further Reading:
+48 601 396 141
