How to Clean and Sanitize Microgreen Trays and Reusable Grow Mediums

You know how to grow microgreens, but are you confident about properly cleaning and sanitizing your trays and grow mediums between harvests? This step is absolutely critical, not just for commercial growers who need to provide safe products to customers, but for home growers who want consistent, healthy results.

Proper sanitation prevents devastating issues like damping off (a fungal disease that can wipe out an entire tray overnight), recurring mold problems, poor germination, and pathogen buildup that affects future grows. After seven years of growing microgreens and testing every cleaning method imaginable, we're sharing exactly what works, what's safe, and what to avoid.

If you're brand new to growing, start with our Beginner's Guide to Growing Microgreens or grab the $3.99 printable Beginner's Guide PDF.

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Quick Answer: How Do You Clean and Sanitize Microgreen Trays and Reusable Grow Mediums?

To clean and sanitize microgreen trays and reusable grow mediums between harvests: first remove all organic material (roots, stems, seed hulls, debris), then wash with hot water and free-and-clear dish soap, rinse thoroughly, and finally sanitize using one of three food-safe methods. The most common sanitizers are 3% hydrogen peroxide (spray and let sit 10 to 20 minutes, no rinsing needed), a bleach solution at 1 tablespoon per gallon of water (10 to 20 minute contact time, rinse thoroughly), or boiling water for 1 to 2 minutes (silicone and stainless-steel mediums only, never plastic trays). Sanitize after every single harvest. Skipping this step is one of the top causes of mold, damping off, and germination problems in microgreens.

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Why Sanitization Matters (Even for Home Growers)

Let's be clear: washing with soap and water removes visible dirt, but it doesn't kill pathogens. Bacteria, fungi, mold spores, and other microorganisms can survive a simple rinse and multiply on your "clean" trays, contaminating your next grow before it even starts.

Even one contaminated tray can spread issues throughout your entire growing area. Mold spores become airborne, fungal diseases transfer through water, and bacterial problems jump from tray to tray. Proper sanitization breaks this cycle and gives each new crop a fresh, clean start. For a deeper look at mold specifically, see our complete mold prevention and identification guide and our damping off prevention guide.

For commercial growers, sanitation isn't optional. It's required by health departments and essential for food safety. But home growers benefit just as much from these practices. A few extra minutes of sanitization prevents hours of troubleshooting mysterious mold problems or dealing with recurring germination failures.

Understanding What Needs Cleaning

Before we dive into methods, let's clarify what we're cleaning:

Plastic Microgreen Trays (mesh trays, no-hole trays, 10x20s, 10x10s, sprouting trays, etc.). These need regular washing and sanitization between grows. Our 10x20 trays, 10x10 trays, and other plastic growing trays all follow the same cleaning protocols.

Reusable Silicone Grow Medium. Our reusable silicone grow medium requires different cleaning methods than plastic trays. (Note: we're phasing out our stainless-steel reusable grow medium and now recommend the silicone version as our primary reusable option.)

Other Equipment. Scissors, harvesting knives, scrapers, spray bottles, and other tools that contact your microgreens should also be sanitized regularly, though we'll focus primarily on trays and mediums in this guide.

Step 1: Remove Debris and Wash (All Materials)

Before any sanitization can work effectively, you must thoroughly remove all organic material. Sanitizers can't penetrate through dirt, roots, and debris. They only work on clean surfaces.

For Plastic Trays:

1. Remove all visible debris. Roots, stems, growing medium residue, seed hulls. Shake out loose material over a compost bin or trash can.
2. Rinse trays under running water to remove loose particles. Warm-hot water works better than cold for loosening stuck-on material.
3. Scrub with a soft brush and free-and-clear dish soap. Pay special attention to corners, edges, and drainage holes where debris accumulates. A dedicated scrub brush works well, nothing fancy needed. Just make sure it's a soft scrub brush that won't scratch up the trays.
4. Rinse thoroughly until all soap residue is gone. Soap left behind can inhibit seed germination in your next grow.

For more on what to do with the root mat and used medium after harvest, see our complete guide on used grow medium.

For the Reusable Silicone Grow Medium:

1. Remove all organic material using our Microgreen Medium Scraper or your hands. Pull out roots, stems, and any remaining plant material. Compost this organic waste.
2. Fill a sink with hot water and food-safe dish soap (we recommend Dr. Bronner's Pure Castile Soap or Seventh Generation Free & Clear Dish Liquid). Let the silicone soak for approximately 20 minutes. Carefully use your hands to gently lather and rinse. Do NOT use brushes or abrasive scrubbers as they can damage the silicone surface or create tiny cuts where bacteria can accumulate. Do NOT stick your hands in very hot water.
3. Rinse thoroughly to remove all soap residue.

Pro Tip: Clean your trays and silicone immediately after harvest while everything is still fresh. Letting root mats dry onto surfaces makes cleanup much harder. We clean ours the same day we harvest, every time.

Pro Tip: Washing reusable silicone grow mediums in batches is way quicker than one at a time. The silicone is also dishwasher safe (top rack only, no heat cycle) for easy maintenance between grows.

Step 2: Sanitize Plastic Trays (Food-Safe Methods)

Now that your trays are physically clean, it's time to kill any remaining pathogens. Here are the food-safe sanitizing methods that actually work:

Method 1: Hydrogen Peroxide (Our Preferred Method)

Hydrogen peroxide is FDA-approved for food contact surfaces, breaks down into just water and oxygen, and is highly effective against bacteria, fungi, and mold spores.

How to use:

• Use standard 3% hydrogen peroxide (the drugstore kind)
• Spray or wipe undiluted 3% solution on all tray surfaces
• Let sit for 10 to 20 minutes for maximum effectiveness
• Allow to air dry. No rinsing needed
• The solution naturally breaks down into water and oxygen

Why we like it: No harsh chemical smell, no toxic residue, environmentally friendly, and doesn't require rinsing. Just spray and let dry.

Where to get it: Any pharmacy, grocery store, or online. Look for standard 3% hydrogen peroxide in the brown bottle.

Method 2: Bleach Solution

Household bleach (sodium hypochlorite) is extremely effective at killing pathogens when used at proper dilutions.

How to use:

• Mix 1 tablespoon of bleach per gallon of water (approximately 200 ppm)
• OR mix 1 part bleach to 9 parts water
• Soak trays for 10 to 20 minutes, OR spray/wipe solution on all surfaces and let sit 10 minutes
• Rinse thoroughly with clean water
• Allow to air dry completely

Important safety notes:

• Always work in a well-ventilated area
• Wear gloves to protect your hands
• Never mix bleach with vinegar or other cleaners (creates toxic fumes)
• Store bleach properly away from heat sources
• Use within recommended timeframes (bleach solutions lose effectiveness over time)

Why it works: Bleach is the gold standard for sanitization and is approved by most health departments. When used at proper dilutions and rinsed well, it's food-safe and highly effective.

Method 3: Commercial Sanitizers

Products like SaniDate, Oxidate, or other EPA-registered sanitizers designed for food contact surfaces are excellent options, especially for commercial operations.

How to use: Follow manufacturer instructions exactly. These products are formulated to specific concentrations and contact times.

Why consider these: Often required or preferred by health departments for commercial operations. Many are hydrogen peroxide-based with stabilizers for extended effectiveness.

Methods to AVOID for Plastic Trays:

❌ Dishwasher "sanitize" cycle. The high heat can warp most plastic trays, ruining them permanently. While dishwashers work for some small items, the heat settings are too aggressive for most microgreen trays.

❌ Boiling water. Will warp and damage plastic trays. Never submerge plastic trays in boiling water or pour boiling water directly on them.

❌ UV sterilization only. While UV light can kill surface pathogens, it doesn't penetrate into crevices or work on shadowed surfaces. UV can supplement other methods but shouldn't be your only sanitization step, especially not for commercial operations.

❌ Vinegar alone. While vinegar has some antimicrobial properties, it's not strong enough to reliably sanitize food contact surfaces. It's fine as a cleaning agent but insufficient for sanitization.

Step 3: Sanitize the Reusable Silicone Grow Medium

The reusable silicone grow medium can handle more aggressive sanitization methods than plastic trays. Our 1.2mm silicone is virgin food-grade platinum-cured silicone with a fiberglass mesh core, FDA compliant per 21 CFR 177.2600, LFGB Tested & Compliant, and rated for 20 to 30+ grow cycles with proper care. Temperature resistance runs from -40°F to 450°F, so it handles boiling water without issue.

You have three approved sanitization options for the reusable silicone grow medium:

Option 1: Boiling Water (Most Thorough)

1. Bring a large pot of water to a rolling boil
2. Carefully submerge the clean silicone in the boiling water
3. Boil for 1 to 2 minutes
4. Remove with tongs and place on a clean surface to cool and air dry
5. Store flat once completely dry

Why this works: Boiling water kills virtually all pathogens instantly. It's the most thorough sanitization method available for silicone. Never touch boiling silicone with bare hands. Always use tongs or heat-resistant utensils.

Option 2: Hot Water Soak (Easiest)

1. Fill a sink with hot water and food-safe dish soap
2. Soak the silicone for approximately 20 minutes
3. Use your hands (no brushes) to gently lather and rinse
4. Rinse thoroughly and air dry

Option 3: Hydrogen Peroxide (No Rinsing Needed)

1. Spray or soak all surfaces with food-grade 3% hydrogen peroxide
2. Let sit for 10 to 20 minutes
3. Air dry. No rinsing needed (hydrogen peroxide breaks down into water and oxygen)

The reusable silicone grow medium is also dishwasher safe (top rack only, no heat cycle).

For a complete walkthrough on the silicone medium itself, see our reusable silicone grow medium launch blog.

Efficient Sanitization Methods for Different Scale Growers

For Home Growers (1 to 10 trays)

The Kitchen Sink Method:

1. Wash trays in your kitchen sink with hot, soapy water
2. Use a dedicated scrub brush
3. Rinse thoroughly
4. Stack trays and spray all surfaces with 3% hydrogen peroxide
5. Let sit for 10 to 20 minutes while you clean up other growing supplies
6. Stack vertically to air dry
7. Store clean, dry trays in a clean area

Time required: About 5 to 10 minutes for a small batch of trays.

Pros: Uses equipment you already have, simple and straightforward, works perfectly for small-scale growing.

Cons: Can be tedious if you have many trays.

For Growing Operations (10 to 50+ trays)

The Reservoir Dunk Method:

1. Set up 2 to 3 large containers (storage totes, buckets, or utility sinks work great)
2. First reservoir: Fill with hot water and dish soap for washing
3. Second reservoir: Fill with clean water for rinsing
4. Third reservoir: Fill with sanitizing solution (hydrogen peroxide or bleach solution)
5. Scrub trays in wash reservoir
6. Dunk in rinse reservoir
7. Dunk in sanitizing reservoir for 10 to 20 minutes
8. Remove and stack vertically to air dry

Time required: About 2 to 5 minutes per tray once you have your system set up.

Pros: Much faster than washing one at a time, efficient use of sanitizer, consistent results.

Cons: Requires space for multiple containers, wash reservoir gets dirty quickly (change water frequently).

For Large Commercial Operations (50+ trays)

The Power Washer Method: This is the fastest method for high-volume tray cleaning, but requires outdoor space and proper equipment.

Setup:

1. Lay clean plastic sheeting or work on clean concrete
2. Stack dirty trays in a designated dirty area
3. Have your sanitizing reservoir ready nearby

Process:

1. Lay out trays on plastic sheeting
2. Power wash trays to remove all debris (rotate to clean both sides)
3. Important: Do NOT use power-washing soap. Most aren't food-safe. Use plain water only
4. After power washing, immediately move trays to sanitizing solution
5. Dunk in sanitizer for required contact time (10 to 20 minutes)
6. Air dry on clean racks

Two-person method: One person power washes while the second person flips trays and moves clean trays to the sanitizing reservoir. This creates an efficient assembly line.

Equipment note: Dedicate a power washer solely to cleaning microgreen trays. Don't use the same power washer you use for driveways, cars, or other non-food applications.

Time required: With two people, you can process 50+ trays in 30 to 45 minutes.

Pros: Fastest method for high volume, very thorough cleaning, scalable.

Cons: Requires outdoor space, power washer investment, weather-dependent.

Understanding Sanitizer Concentrations and Safety

Different regions and health departments have varying requirements for sanitizer concentrations. Here's what you need to know:

Bleach (Sodium Hypochlorite)

Recommended concentration: 50 to 200 ppm (parts per million)
Common mixing ratios: 1 tablespoon per gallon of water, OR 1 part bleach to 9 parts water
Contact time: 10 to 20 minutes minimum
Rinse required: Yes, always rinse thoroughly after bleach sanitization

Safety reminder: Bleach concentrations above 200 ppm can leave toxic residue and may damage materials over time. More is not better. Stick to recommended ratios.

Hydrogen Peroxide

Concentration: 3% solution (standard drugstore strength)
Application: Use undiluted for sanitization
Contact time: 10 to 20 minutes
Rinse required: No, breaks down into water and oxygen

For commercial operations: You may need food-grade hydrogen peroxide (not the stabilized drugstore version). Check with your local health department.

Measuring PPM

If your health department requires specific PPM measurements, you'll need a PPM testing pen which can be found on our Amazon storefront. These inexpensive devices let you verify your sanitizer concentration is within approved ranges.

Critical: Know Your Local Requirements

This is extremely important: Health department requirements for sanitization vary significantly by county, state, and region. What's approved in one location may not be acceptable in another. The FDA Produce Safety Rule provides federal guidance, but local requirements often go further.

Before you start any commercial microgreen operation:

1. Contact your local health department
2. Ask for specific sanitation guidelines for growing and selling produce
3. Find out which sanitizers are approved
4. Learn the required concentrations (PPM levels)
5. Understand required contact times
6. Ask about documentation requirements

For commercial growers selling to restaurants, also read our Best Microgreens for Restaurants guide, which covers food safety considerations in more detail.

For home growers: While you're not subject to health department regulations if you're growing for personal use, following these professional standards ensures the healthiest, safest microgreens for you and your family.

Common Sanitization Mistakes to Avoid

For a broader look at microgreen growing mistakes, see our top microgreen growing mistakes guide.

Mistake #1: Sanitizing dirty trays. Sanitizers only work on clean surfaces. If you spray sanitizer on trays covered in debris, you're just wetting dirty trays. Always wash thoroughly first.

Mistake #2: Not allowing proper contact time. Sanitizers need time to work, usually 10 to 20 minutes. Spraying and immediately rinsing defeats the purpose.

Mistake #3: Using expired or improperly stored sanitizers. Bleach solutions lose effectiveness within 24 hours of mixing. Hydrogen peroxide degrades when exposed to light (that's why it comes in brown bottles). Always mix fresh and store properly.

Mistake #4: Skipping sanitization because trays "look clean." Pathogens are invisible. A tray can look perfectly clean and still harbor bacteria, fungi, and mold spores.

Mistake #5: Using too much sanitizer. More concentrated doesn't mean more effective. Excessive sanitizer can leave residue that inhibits seed germination or creates food safety issues. Follow recommended ratios.

Mistake #6: Not sanitizing often enough. Sanitize between every grow, not just when you see mold. Prevention is much easier than fixing contamination issues.

Storage Best Practices

After sanitization, proper storage prevents re-contamination:

For Trays:

• Store in a clean, dry area away from potential contamination sources
• Stack with a barrier (clean towel or plastic) between stacks to prevent dust accumulation
• Keep away from areas with standing water, soil, or outdoor air
• Consider storing in closed bins or covered shelves

For the Reusable Silicone Grow Medium:

• Store completely flat to maintain shape
• Keep in a clean, dry location
• We store ours in a dedicated tray to keep them flat and organized and place it on the very top shelf where debris cannot get on them
• Avoid folding or creasing
• Keep away from sharp objects that might cut or tear

Supplies That Make Sanitization Easier

Essential:

• Scrub brush dedicated to tray cleaning
• Spray bottles for sanitizer
• Gloves for handling sanitizers
• Large containers or tote bins for reservoir dunking method
• Our Microgreen Medium Scraper for the reusable silicone grow medium

Optional but helpful:

• PPM testing pen (required for some commercial operations, available on our Amazon storefront)
• Drying rack for organizing clean trays
• Power washer (for large operations)
• Multiple spray bottles labeled for different sanitizers
• Timer to track contact times

Frequently Asked Questions About Cleaning and Sanitizing Microgreen Trays

How do you sanitize microgreen trays?

First wash trays with hot water and free-and-clear dish soap, scrubbing with a soft brush to remove all debris and root residue. Then rinse thoroughly. Finally, sanitize using one of three food-safe methods: spray with 3% hydrogen peroxide and let sit for 10 to 20 minutes (no rinsing needed), soak in a bleach solution at 1 tablespoon per gallon of water for 10 to 20 minutes then rinse thoroughly, or use a commercial food-safe sanitizer like SaniDate or Oxidate following label directions. Never use boiling water or the dishwasher's sanitize cycle on plastic trays. They'll warp.

How often should I sanitize my microgreen trays?

After every single harvest, no exceptions. Sanitization between every grow prevents pathogen buildup and ensures consistent results. Skipping sanitization is one of the top causes of recurring mold problems, damping off, and poor germination in microgreens.

Can you put microgreen trays in the dishwasher?

No, not on the sanitize or heated dry cycle. The high heat warps most plastic microgreen trays permanently. However, the reusable silicone grow medium IS dishwasher safe on the top rack only with no heat cycle. For plastic trays, stick with hand washing and food-safe sanitizers like hydrogen peroxide or diluted bleach.

What is the best sanitizer for microgreens?

Our preferred sanitizer is 3% hydrogen peroxide from any drugstore. It's FDA-approved for food contact surfaces, kills bacteria, fungi, and mold spores, requires no rinsing, breaks down into water and oxygen, and has no harsh chemical smell. For commercial operations or anyone who prefers a more aggressive option, household bleach at 1 tablespoon per gallon of water also works well but requires thorough rinsing.

How do you sanitize the reusable silicone grow medium?

You have three options for the reusable silicone grow medium: boiling water for 1 to 2 minutes (most thorough), a hot soapy water soak for 20 minutes (easiest), or spraying with 3% hydrogen peroxide for 10 to 20 minutes (no rinsing needed). The silicone is also dishwasher safe on the top rack with no heat cycle. Never use brushes or abrasive scrubbers on silicone. They can damage the surface and create tiny cuts where bacteria accumulate. Hands and soap only.

Can I use vinegar to clean microgreen trays?

Vinegar works as a cleaning agent to remove buildup, but it's not strong enough to reliably sanitize food contact surfaces against bacteria, fungi, and mold spores. Use vinegar for general cleaning if you want, but always follow up with a proper food-safe sanitizer like hydrogen peroxide or diluted bleach. And never mix vinegar with bleach, which produces toxic fumes.

How long do I need to sanitize microgreen trays?

Most food-safe sanitizers require 10 to 20 minutes of contact time to effectively kill pathogens. Spraying and immediately rinsing or wiping defeats the purpose. Let the sanitizer sit on the surface for the full contact time, then either rinse thoroughly (for bleach) or air dry (for hydrogen peroxide).

Do I need to sanitize my harvesting scissors and tools?

Yes. Cross-contamination from tools is a real issue, especially when harvesting multiple trays in one session. Wipe down scissors, knives, and the Microgreen Medium Scraper with 3% hydrogen peroxide or dip in your sanitizing solution between harvests. This is especially important for commercial growers and anyone who's had mold or disease issues recently.

Can I use the same sanitizer for trays and reusable mediums?

Yes. 3% hydrogen peroxide works on both plastic trays and the reusable silicone grow medium. Bleach solution also works on both, but always rinse thoroughly after bleach. Boiling water is the one method that's different. Use it for silicone (handles up to 450°F) but never for plastic trays (warps them).

What happens if I skip sanitization?

Skipping sanitization is one of the top causes of recurring problems in microgreen growing: persistent mold issues, damping off (a fungal disease that wipes out entire trays), patchy or failed germination, and pathogen buildup that gets worse with each grow. Five minutes of sanitization per tray prevents days of troubleshooting and crop losses. It's the single highest-leverage habit a microgreen grower can build.

Building Sanitization Into Your Routine

The key to consistent sanitization is making it a non-negotiable part of your growing routine, not something you do "when you have time" or "when you remember."

Our routine:

1. Harvest microgreens in the morning or afternoon
2. Remove root mats and dispose/compost immediately
3. Wash and sanitize all trays and reusable silicone grow mediums from that harvest
4. Let trays and silicone air dry while we go about our day
5. Store clean, dry trays and silicone before the next planting session

By handling it immediately after harvest, it becomes automatic. Letting dirty trays pile up makes the whole process feel overwhelming and increases the chance you'll skip sanitization.

Final Thoughts

Proper cleaning and sanitization might not be the most exciting part of growing microgreens, which is why you barely see any videos or posts on the topic, but it's absolutely foundational to success. Five minutes of sanitization per tray prevents days of troubleshooting disease issues, wasted seeds, and crop losses.

Whether you're a home grower producing a few trays for your family or a commercial operation supplying restaurants and farmers markets, these food-safe sanitization practices protect your crops, your customers, and your reputation.

Start with the method that fits your scale, commit to sanitizing between every grow, and you'll see the difference in your germination rates, plant health, and overall consistency.

Clean trays = healthy microgreens = happy growers. It's that simple.

For more detailed growing guidance, check out our other resources:

• Free Microgreen Troubleshooting, FAQ & Lingo PDF
• What To Do With Used Grow Medium After Harvesting Microgreens
• Microgreen Masterclass Course
• On The Grow Video Library

Happy growing (and happy sanitizing)! 🌱

-CJ & Mandi

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Related Blogs You Might Enjoy

• How to Start Growing Microgreens: A Beginner's Guide
• How to Grow Broccoli Microgreens
• What to Do With Used Microgreen Grow Medium After Harvest
• Why Are My Microgreens Moldy? Mold vs. Root Hairs Guide
• What Is Damping Off and How to Prevent It
• Top Microgreen Growing Mistakes and How to Avoid Them
• Meet Our Reusable Silicone Grow Medium
• Which Microgreen Seeds Work on Reusable Grow Mediums?
• Why We Don't Eat Microgreen Roots Like Sprouts
• Best Microgreen Growing Advice and Resources

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Published: January 2026
Updated: May 23, 2026
All content is property of On The Grow®, LLC