How to Clean and Sanitize Microgreen Trays and Reusable Grow Mediums: Complete Guide

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.

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 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-holed trays, 10x20s, 10x10s, sprouting trays, etc.) - These need regular washing and sanitization between grows. The Bootstrap Farmer trays and other plastic growing trays all follow the same cleaning protocols.

Reusable Grow Mediums - Our Silicone Reusable Grow Medium and Stainless-Steel Reusable Grow Medium require different cleaning methods than plastic trays.

Other Equipment - Scissors, harvesting knifes, 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 brush and dish soap (we use free and clear ). Pay special attention to corners, edges, and drainage holes where debris accumulates. A dedicated scrub brush works well—nothing fancy needed. Just make sure that its a soft scrub brush, that wont 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 Reusable Mediums:

1. Remove all organic material using our Microgreen Medium Scraper/Cleaner or your hands. Pull out roots, stems, and any remaining plant material. Compost this organic waste.
2. For Silicone: Fill a sink with hot water and food-safe dish soap (we recommend Dr. Bonner's Pure Castile Soap or Seventh Generation Free & Clear Dish Liquid). Let the silicone soak for approximately 20 minutes. 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.
3. For Stainless Steel: Rinse under running warm water. You can use a brush to scrub away stubborn debris if needed. Wash with warm water and free-and-clear dish soap, then rinse very thoroughly.

Pro Tip: Clean your trays and mediums 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 grow mediums in batches is way quicker than one at a time.

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 10-20 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 10-20 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 Reusable Grow Mediums

Reusable grow mediums can handle more aggressive sanitization methods than plastic trays. Here's how to properly sanitize each type:

Silicone Reusable Grow Medium

Our Silicone Reusable Grow Medium can withstand high temperatures, making boiling water the most effective sanitization method.

Boiling Water Method (Recommended):

1. Bring a large pot of water to a rolling boil
2. Carefully submerge the clean silicone sheets in the boiling water
3. Boil for 1-2 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.

Alternative - Hydrogen Peroxide: If boiling isn't convenient, you can also use 3% hydrogen peroxide:

1. Spray or wipe all surfaces with undiluted 3% hydrogen peroxide
2. Let sit for 10-20 minutes
3. Air dry (no rinsing needed)

Stainless-Steel Reusable Grow Medium

Our Stainless-Steel Reusable Grow Medium is incredibly durable and can handle multiple sanitization methods.

Boiling Water Method:

1. Submerge clean stainless-steel sheets in boiling water for 1-2 minutes
2. Remove carefully (the metal will be very hot!)
3. Let cool and air dry completely
4. Store flat

Hydrogen Peroxide Method:

1. Spray or wipe with 3% hydrogen peroxide solution
2. Let sit for 10-20 minutes
3. Air dry (no rinsing needed)

Bleach Solution Method:

1. Soak in bleach solution (1 tablespoon per gallon of water) for 10-20 minutes
2. Rinse thoroughly with clean water
3. Air dry completely

Why stainless steel is versatile: The 316-grade stainless steel we use is corrosion-resistant and can handle bleach, hydrogen peroxide, and high heat without degrading.

Efficient Sanitization Methods for Different Scale Growers

For Home Growers (1-10 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 10-20 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 5-10 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 (10-50+ trays)

The Reservoir Dunk Method:

1. Set up 2-3 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 10-20 minutes
8. Remove and stack vertically to air dry

Time required: About 2-5 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 (10-20 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 30-45 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: 50-200 ppm (parts per million) Common mixing ratios: 1 tablespoon per gallon of water, OR 1 part bleach to 9 parts water Contact time: 10-20 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: 10-20 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 Amazon. 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.

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 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

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 10-20 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 Reusable Mediums:

• 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 can not get on them
• Avoid folding or creasing, especially stainless steel
• 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/Cleaner for reusable mediums

Optional but helpful:

• PPM testing pen (required for some commercial operations)
• 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

How often should I sanitize my trays? After every single harvest. No exceptions. Sanitization between every grow prevents pathogen buildup and ensures consistent results.

Can I sanitize multiple trays at once? Yes! The reservoir dunk method lets you sanitize many trays simultaneously. Just ensure each tray is fully submerged and makes contact with the sanitizing solution for the full contact time.

What if I forget to sanitize and use a tray immediately? If you catch it before seeding, sanitize the tray properly and let it dry completely before use. If you've already seeded, watch that tray extra carefully for any signs of disease. Going forward, build sanitization into your routine so it never gets skipped.

Do I really need to rinse after using bleach? Yes, always. Bleach residue can inhibit seed germination and isn't safe for food contact surfaces without rinsing.

How do I know if my sanitizer is still effective? Bleach solutions should be mixed fresh daily—they lose effectiveness within 24 hours. Hydrogen peroxide in brown bottles stays effective until the expiration date if stored properly. Commercial sanitizers have expiration dates on their labels.

What about sanitizing scissors and harvest tools? Yes! Wipe down with hydrogen peroxide or dip in your sanitizing solution between harvests, especially if you're harvesting multiple trays. Cross-contamination from tools is a real issue.

Can I use the same scrub brush for trays and dishes? We recommend a dedicated brush for microgreen trays to prevent any potential cross-contamination. It's a small investment that adds peace of mind.

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 mediums from that harvest
4. Let trays and mediums air dry while we go about our day
5. Store clean, dry trays and mediums 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 Microgreens After Harvest: Complete Disposal Guide
• Microgreen Masterclass Course
• YouTube Channel @onthegrow

Happy growing (and happy sanitizing)! 🌱

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