How to Clean and Sanitize Microgreen Trays Between Crops

Washing is necessary, but it is not the same as sanitizing. Visible soil, plant material, and residue can interfere with sanitizer performance, so sanitizing should happen only after the tray has been thoroughly cleaned. University of Minnesota Extension

This guide covers reusable 1020 trays, drain trays, solid bottom trays, covers, weights, and similar reusable growing equipment. It does not cover seed treatment, water-system cleaning, microbial testing, or diagnosing mold in a crop.

Used trays can retain roots, growing media, seed hulls, mineral residue, and moisture—especially around rims, corners, undersides, drainage holes, and surfaces where trays nest together.

A consistent cleaning and sanitation routine helps reduce the chance that residue from one crop carries into the next. Microgreen-production guidance identifies cleaning and sanitizing reusable equipment between crop cycles as an important production-hygiene practice. Virginia Cooperative Extension

Still, tray hygiene is only one part of safer microgreen production. Seeds, growing media, water, tools, harvesting practices, storage, and hand hygiene also matter. A properly cleaned and sanitized tray can reduce equipment-hygiene risks, but it cannot guarantee a safe crop or prevent every mold problem.

These terms are often used as though they mean the same thing. They do not.

The U.S. Environmental Protection Agency distinguishes between cleaning, sanitizing, and disinfecting based on what a product is intended to do and how it is used. EPA

Cleaning is the physical work of removing debris from the tray. This includes spent roots, growing media, seed hulls, mineral film, and buildup around drain holes or tray rims.

A quick rinse may remove loose material, but it is not a complete cleaning step. The FDA Food Code uses the standard “clean to sight and touch” for food-contact surfaces. While the Food Code is a model for retail and food-service settings rather than a microgreen-tray regulation, it is a useful practical inspection benchmark. FDA Food Code

Pay particular attention to:

Sanitizing should not be used as a shortcut around washing and scrubbing. Spraying sanitizer over roots, soil, or visible residue does not replace the cleaning process.

Use a sanitizer only according to its label for the intended surface and application. Where relevant, look for food-contact-surface directions. The label determines important details, including:

EPA guidance for food-contact-surface sanitizers makes clear that dilution, wet contact time, rinsing, and drying directions are product-specific. EPA food-contact-surface labeling guidance

Disinfecting is not simply another word for sanitizing. Some products may carry both sanitizer and disinfectant claims, but the approved uses and instructions depend on the individual label.

For routine tray hygiene, do not assume that any household disinfectant is appropriate for reusable growing equipment. Follow the product label for the surface, use, contact time, and any post-treatment instructions. EPA

A sanitized tray is not necessarily sterile. The practical goal is a tray that has been thoroughly cleaned, sanitized according to applicable label directions, fully dried, and stored so it is not recontaminated before the next crop.

Set up the cleaning area before bringing in used trays.

Read the product label before using it. Confirm:

Do not assume a tray is dishwasher-safe or compatible with a particular cleaning method; check its manufacturer care guidance and the sanitizer label.

Create a clear path from dirty trays to clean, dry storage.

Keep used trays, spent media, roots, and dirty cleaning tools on one side of the work area. Move washed and sanitized trays toward a separate drying and storage area. This helps prevent a cleaned tray from being set back onto a dirty table or exposed to splash from used trays.

Storing cleaned equipment in a clean, dry area protected from contamination is consistent with FDA Food Code hygiene principles. FDA Food Code

Remove all visible material before rinsing or sanitizing, including:

Scrape or brush out the tray thoroughly. Check the underside, rims, corners, drain holes, and edges that contact other trays when stacked.

If you grow in a drain-hole tray placed inside a solid bottom tray, include both trays in the routine. The lower tray can accumulate water and debris during a crop cycle, so cleaning it is a sensible part of the equipment reset.

Rinse the tray to remove loose debris before washing it with detergent.

Use this step to flush hard-to-reach areas, including:

Pre-rinsing helps make scrubbing more effective, but it does not replace washing.

Wash the tray with detergent and water, then scrub all surfaces with a dedicated brush.

Focus on residue-prone areas:

Detergent and scrubbing are the cleaning step. They remove soil and residue that could limit sanitizer contact, but they are not the same as sanitizing. University of Minnesota Extension

Rinse away detergent and loosened residue before sanitizing.

If you can still see roots, media, seed hulls, or residue after rinsing, return to the wash-and-scrub step. Sanitizer should be applied to a physically clean surface.

Inspect trays under good light before sanitizing.

A tray is ready when it has:

The FDA’s “clean to sight and touch” standard is a useful check before the sanitation step. FDA Food Code

Apply sanitizer only after the tray is clean.

Follow the individual product’s directions for:

Keep the surface wet for the full label-required contact time. A quick spray followed by immediate draining or wiping may not meet the product’s instructions. EPA food-contact-surface labeling guidance

When your sanitation method requires concentration verification, use the appropriate test strips or other approved test method. This is especially useful for growers mixing sanitizer regularly or cleaning larger numbers of trays. The FDA Food Code similarly calls for a test kit or device that can accurately measure sanitizer concentration in its food-establishment context. FDA Food Code

After sanitizing, follow the product label’s directions for draining, rinsing if required, and drying.

Let trays air-dry on a clean rack or clean surface. Avoid towel-drying sanitized equipment, since towels and handling can reintroduce contamination. University of Minnesota Extension

Do not stack or nest trays while they are still wet. FDA Food Code guidance notes that wet stacking can slow drying and create conditions that may support microbial growth. FDA Food Code

Once dry, store trays away from:

There is no single sanitizer type, brand, concentration, or contact time that is universally appropriate for every tray and growing setup.

Choose a product based on its label, intended use, and directions for the relevant surface. Do not substitute a social-media recipe, generic dilution chart, or advice meant for a different product.

Sanitizer performance depends on correct preparation and sufficient wet contact time.

Avoid:

EPA labeling requirements make these details product-specific. EPA food-contact-surface labeling guidance

Some sanitizers may direct users to drain and air-dry a surface. Others may require a potable-water rinse after the required contact time.

There is no universal “always rinse” or “never rinse” rule. Follow the individual product label. EPA food-contact-surface labeling guidance

For systems that require concentration verification, test strips or another appropriate test method can help confirm that a sanitizer solution is within its usable range.

This can be particularly useful when:

Use the verification method designed for your specific sanitizer system.

Before using a dishwasher, high heat, or a chemical method, check the tray manufacturer’s care guidance and the sanitizer label. Do not assume a tray is dishwasher-safe or compatible with a particular cleaning method.

Vinegar should not be presented as a substitute for a properly labeled sanitizer in a between-crop tray routine. University of Minnesota Extension specifically states that vinegar is not an acceptable sanitizer for produce-related tools, containers, and surfaces. University of Minnesota Extension

Rinsing, detergent, and scrubbing are important cleaning steps. They remove debris and prepare a tray for sanitizing. But cleaning with soap or detergent is not the same as completing a label-directed sanitizing step. EPA

Do not assume that one bleach, hydrogen peroxide, quaternary ammonium, or peroxyacetic-acid recipe is suitable for every tray and growing setup.

The correct method depends on the specific product label, intended use, tray material, application method, water conditions, contact time, and post-treatment directions.

A dishwasher may be suitable for some trays if the manufacturer says so, but it should not be assumed to meet the sanitation needs of every reusable tray. Check the manufacturer’s care instructions, then follow the sanitizer label when a sanitation step is needed.

Avoid these frequent errors:

Do not return a tray to routine use if visible residue remains after normal washing, or if it has an odor that persists after cleaning.

Repeat the wash-and-rinse steps as needed, then inspect and sanitize the tray according to product directions. If it cannot be brought to a visibly clean condition, set it aside for further assessment rather than using it for the next crop.

A persistent odor is an inspection concern, not proof of a particular microbial hazard.

As a practical hygiene principle, reusable trays should remain reasonably smooth, accessible, and easy to inspect. Set aside trays with:

FDA Food Code equipment standards emphasize surfaces that are smooth, accessible, and resistant to deterioration because those features support effective cleaning. Applying that principle to reusable growing trays is practical guidance, not a formal microgreen-specific replacement rule. FDA Food Code

Replace a tray when its condition prevents effective cleaning and inspection—not after a fixed number of crop cycles.

If you suspect an unusual contamination event, pause routine reuse of affected trays and related equipment. Seek operation-specific guidance from a local extension service or food-safety authority before resuming normal use.

This article does not provide a testing, disposal, or incident-response protocol. One extra wash-and-sanitize cycle should not be treated as a guarantee that every potential concern has been resolved.

For home growers, consistency matters more than complexity:

Keep the routine simple enough that you will do it after every crop rather than only when trays look visibly dirty.

Growers selling microgreens can benefit from a written sanitation standard operating procedure, or SOP. Penn State Extension recommends written procedures so workers understand food-safety expectations in microgreen production. Penn State Extension

A simple tray-cleaning log can include:

FDA sprout guidance offers useful sanitation-policy and recordkeeping examples, but sprout requirements should not be treated as automatic legal requirements for every microgreen grower. Sprouts and microgreens are not identical products, and applicable obligations can vary by location and business. FDA sprout guidance

https://www.fda.gov/food/retail-food-protection/fda-food-code

https://www.fda.gov/media/102430/download

https://www.ecfr.gov/current/title-21/chapter-I/subchapter-B/part-112/subpart-M/section-112.143

https://www.epa.gov/coronavirus-and-disinfectants/whats-difference-between-products-disinfect-sanitize-and-clean

https://www.epa.gov/sites/default/files/2020-04/documents/label_requirements_for_pesticides_used_for_sanitation_of_food_contact_surfaces.pdf

https://www.epa.gov/pesticide-labels/pesticide-labeling-questions-answers

https://extension.umn.edu/agriculture/farm-operations-and-systems/on-farm-food-safety/cleaning-and-sanitizing-tools-harvest-containers-and-surfaces

https://extension.psu.edu/ensuring-food-safety-in-microgreens-production

https://www.pubs.ext.vt.edu/content/dam/pubs_ext_vt_edu/spes/spes-756/SPES-756.pdf

https://www.uvm.edu/extension/necafs/indoor-growing-legacy-greens

https://andisway.com/products/growing-trays-with-drain-holes