What to Do With Used Microgreen Grow Medium After Harvest
You've just harvested a beautiful tray of microgreens, congratulations! Your fresh greens are ready to eat, and you're probably feeling pretty accomplished. But now you're staring at a tray full of roots, stems, and growing medium wondering: "What exactly am I supposed to do with all this stuff?"
This is honestly one of the top questions we receive through our YouTube channel, website, and social media. And it makes sense, nobody really talks about the cleanup phase when they're showing off their gorgeous harvest photos. The truth is, what you do with your leftovers depends entirely on what type of growing medium you're using. Let's break down your options for each type of medium so you can handle cleanup efficiently and make choices that work for your situation.
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.
Quick Answer: What Do You Do With Used Grow Medium After Harvesting Microgreens?
What you do with used microgreen grow medium depends on the type of medium. Soil, coco coir, hemp mats, and other plant-based mediums are compostable, lift out of the tray as a "root mat," and can go straight into a backyard compost bin or municipal green waste collection. Finished compost from microgreen root mats should be used in outdoor gardens only (not for growing new microgreens) due to pathogen risk. Reusable silicone and stainless-steel grow mediums get cleaned, sanitized (boiling water for silicone, hydrogen peroxide for stainless steel), and reused for the next grow. Perlite and vermiculite are technically reusable but rarely worth the labor. The most eco-friendly option for most home growers is to compost disposable mediums or invest in a reusable silicone grow medium that lasts for 20 to 30+ grow cycles.
Understanding What You're Dealing With: The "Root Mat"
Before we dive into disposal methods, let's talk about what's actually left in your tray after harvest. When you cut microgreens above the soil line, you leave behind what we call the "root mat." A dense network of roots, unharvested stems, seed hulls, and whatever growing medium you used. This root mat is surprisingly compact and holds together as one piece in most cases, making it relatively easy to remove from your tray.
The root mat contains organic material (the plant roots and stems) mixed with your growing medium. How you handle this depends entirely on what that medium is made of. For more on why we harvest above the root line and never eat microgreen roots, see our blog on why we don't eat microgreon roots like sprouts.
Soil-Based Growing Medium: Composting Is Your Best Friend
If you're growing in potting soil or seed starting mix, you have one of the easiest cleanup situations. Soil-based mediums are completely compostable and actually add valuable organic matter to your compost system.
The Process:
After harvest, simply remove the entire root mat from your tray. It usually lifts out as one solid piece. Toss it directly into your compost bin where organisms and microorganisms will break it down over time (typically 2 to 10 months depending on your composting conditions and climate).
Once the root mat has fully decomposed and you have finished compost, you can use it in your outdoor garden beds. We specifically say "outdoor garden only" for an important reason: there's a higher chance of pathogens being present in composted grow medium, so we prefer really clean, fresh medium for growing microgreens. But for outdoor vegetable gardens, flower beds, or landscaping? It's perfect.
Don't Have a Compost Bin?
No problem. You have a few options:
The "toss it in the yard" method: Simply throw the root mat somewhere in your yard and either mow over it or just let nature do its thing. Is this the most elegant solution? Nope. Can it make your yard look a bit weird temporarily? Sure. Are we guilty of doing this in the past? Absolutely. The organic material will eventually break down and return to the earth. Just avoid doing this in high-visibility areas of your yard.
The accidental permaculture method: We once created an entire permaculture area in our yard completely by accident from leftover microgreen seeds that germinated late and grew into full adult plants. It actually looked pretty cool, and the bees loved it. Sometimes "disposal mistakes" turn into happy accidents.
Municipal green waste collection: Many cities offer green waste or yard waste collection. Your microgreen root mats would be perfect for this service if available in your area.
Community gardens or friends with compost: Know someone who composts? They'd probably love your microgreen leftovers as "green material" for their compost pile.
Our Current Setup:
We use a compost bin for all our microgreen leftovers. The setup was extremely quick and easy, and it handles our volume perfectly. If you're generating a lot of microgreen leftovers, having a dedicated composting solution makes the whole process seamless. There are many great options available depending on your space and needs, from small countertop bins for apartment dwellers to large outdoor tumblers for serious growers. Browse our Amazon storefront for the composting setups we recommend.
Coco Coir: Compostable With Considerations
Coco coir is another compostable option, though it breaks down somewhat differently than soil. Made from coconut husks, coco coir is completely organic and biodegradable. We no longer sell coco coir directly, but if you need some, here's the coco coir we recommend on our Amazon storefront.
The Process:
Remove your root mat from the tray and add it to your compost bin just like you would with soil. Coco coir can take slightly longer to break down than traditional soil, but it will eventually decompose completely. Some growers report that coco coir adds excellent structure to finished compost.
Alternative Uses:
Because coco coir is relatively clean and breaks down slowly, some gardeners actually prefer to use spent coco coir directly in outdoor garden beds as a soil amendment without fully composting it first. It helps with moisture retention and adds organic matter to the soil. You can mix it into garden soil, use it as mulch, or add it to outdoor container plantings.
The Reuse Question:
Technically, you could attempt to separate the roots from the coco coir, sterilize the coco, and reuse it. However, in our experience, this process is more trouble than it's worth. The roots become so intertwined with the coco fibers that separation is tedious, and even after sterilization, you risk introducing pathogens into future grows. Fresh coco coir is affordable enough (especially when you buy compressed bricks) that starting fresh each time is the practical choice.
Hemp and Other Biodegradable Grow Mats: Composting Works
If you're using hemp mats, jute mats, or other plant-based hydroponic grow mats, these are fully compostable just like soil and coco coir.
The Process:
Remove the mat with all the roots and organic material attached, and toss it directly into your compost bin. These materials will break down over time, though the rate depends on the specific mat type and your composting conditions. Hemp mats tend to decompose relatively quickly, while some denser mats may take longer.
What About Biostrate?
Biostrate is a special case. While it's made from biodegradable materials, it requires industrial composting facilities to properly break down. Standard backyard compost bins don't generate enough heat to decompose Biostrate effectively. If you're using Biostrate and want to dispose of it responsibly, check if your area has industrial composting facilities that accept it. Otherwise, it will need to go in the trash.
Reusable Silicone Grow Medium: Cleaning and Sanitizing for Next Use
If you're using our reusable silicone grow medium, the cleanup process is different. That's the whole point of reusable mediums. Instead of disposal, you're cleaning for the next grow.
Note: We're phasing out our stainless-steel reusable grow medium and now recommend the silicone version as our primary reusable option. The 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.
For a deeper dive into the silicone medium, see our reusable silicone grow medium launch blog and our complete cleaning and sanitization guide.
Step 1: Remove Organic Material
Pull out or scrape off all the leftover microgreen roots and stems. These should come off relatively easily. We designed our Microgreen Medium Scraper specifically for this purpose. It makes quick work of root removal without damaging the medium.
Compost or dispose of these organic leftovers (they're just plant roots and stems, so compost them like you would any other plant material).
Step 2: Wash Thoroughly
Rinse the reusable silicone grow medium under running water and remove any remaining debris. The goal is to remove all organic material completely. Then wash it with a free-and-clear dish soap (Dr. Bronner's or Seventh Generation work great) using your hands. Avoid brushes or abrasive scrubbers that can damage the silicone. Rinse thoroughly to remove all soap residue.
Step 3: Sanitize
This step is critical and non-negotiable. Even if your medium looks clean, you must sanitize it between grows to prevent pathogen buildup.
You have three sanitization options for the reusable silicone grow medium:
- Boiling water: Submerge the silicone in boiling water for 1 to 2 minutes. Use tongs or heat-resistant utensils. Never touch boiling silicone with bare hands. Allow to cool completely before handling.
- Hot water soak: Fill a sink with hot water and food-safe dish soap and soak the silicone for approximately 20 minutes.
- Hydrogen peroxide: Spray or soak the medium with food-grade 3% hydrogen peroxide for 10 to 20 minutes. 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 easy maintenance between grows.
Important: Never use boiling water on plastic trays. It will warp them. The boiling water method is only for silicone and stainless-steel grow mediums.
How Long Does the Reusable Silicone Grow Medium Last?
With proper cleaning and sanitization, our 1.2mm reusable silicone grow medium is rated for 20 to 30+ growing cycles, or roughly 18 to 24 months of regular use. Some seed varieties (especially red varieties or seeds with natural pigments) may cause cosmetic staining on the silicone surface, but this doesn't affect performance. Replace your silicone when you see visible tears, deep cuts, loss of flexibility, or significant physical damage. The upfront cost is higher than disposable mediums, but the long-term savings and environmental benefits are significant.
Perlite, Vermiculite, and Other Inorganic Mediums: Difficult to Reuse
Some growers use perlite, vermiculite, or similar inorganic mediums for hydroponic microgreen production. While technically reusable, the process is labor-intensive and comes with risks.
The Reuse Process (If You Really Want To):
- Separate the organic material (roots and stems) from the medium. This requires screening through a mesh that catches the organic matter while letting the perlite/vermiculite pass through. It's tedious work.
- Compost or dispose of the separated organic material.
- Sterilize the medium by baking it in an oven. Spread about 4 inches deep in an oven-safe pan, cover with foil, and bake at 180 to 200°F (82 to 93°C) for at least 30 minutes, or until the medium reaches 180°F throughout.
Critical Safety Note: Never exceed 200°F when baking growing medium. Higher temperatures can cause it to produce toxins.
- Let cool completely before reuse.
Our Honest Opinion:
We don't recommend this method. It's time-consuming, uses significant energy, and even with sterilization, there's potential for pathogens to survive. Plus, perlite and vermiculite are inexpensive enough that the time and effort spent on sterilization usually isn't worth it. Most commercial growers use fresh medium for each crop, and we think home growers are better off doing the same.
If you want a reusable option, our purpose-designed reusable silicone grow medium is far easier to clean and sanitize between uses.
What About Just Throwing It in the Trash?
Look, we're not going to judge you if you occasionally toss a root mat in the trash. Sometimes you're in a hurry, or you don't have composting options available, or you're dealing with a moldy tray you'd rather not add to your compost. It happens. (If mold has been a recurring issue, our complete mold prevention and identification guide walks through how to avoid it next time.)
However, from both an environmental and practical perspective, composting is almost always the better choice. Organic waste in landfills breaks down anaerobically (without oxygen), producing methane, a potent greenhouse gas. In a compost bin or in your yard, that same organic material breaks down aerobically and eventually becomes nutrient-rich soil amendment.
If you truly have no way to compost (no yard, no municipal green waste collection, no community garden access), then trash disposal is your only option. But if composting is at all possible, it's worth the minimal extra effort.
Our Personal Philosophy and Recommendation
After growing microgreens for seven years and testing every method imaginable, here's what we've landed on:
For disposable mediums (soil, coco coir, hemp mats): We prefer starting each grow with fresh medium and composting after harvest. This ensures our growing medium is clean every time, eliminates the need for complicated sterilization procedures, and produces amazing finished compost for our outdoor gardens. The time saved by not trying to reuse disposable mediums is worth way more than the cost of fresh medium.
For reusable mediums (silicone): Absolutely worth using if you commit to proper cleaning and sanitization between grows. The initial investment pays off over time, and the environmental benefits are significant.
Never recommended: Attempting to sterilize and reuse perlite, vermiculite, or similar inorganic mediums. The juice just isn't worth the squeeze in our opinion.
Environmental Considerations
If you're growing microgreens, there's a good chance you care about sustainability and environmental impact. Here's how different disposal methods stack up:
Most Eco-Friendly:
- Composting disposable mediums and reusing the finished compost
- Using properly maintained reusable grow mediums
- Returning organic material directly to your yard
Less Eco-Friendly:
- Landfill disposal of compostable materials
- Energy-intensive sterilization methods for questionable reuse
The good news? The most eco-friendly options are also usually the most convenient and cost-effective. It's a win-win situation.
Frequently Asked Questions About Used Microgreen Grow Medium
What do you do with leftover soil after growing microgreens?
Compost it. After harvest, lift the entire root mat (roots, stems, seed hulls, and soil) out of the tray as one piece and add it to your backyard compost bin or municipal green waste collection. It takes 2 to 10 months to fully break down. Once it's finished compost, use it in outdoor garden beds (vegetables, flowers, landscaping), not for growing new microgreens.
Can you reuse soil from microgreens?
We don't recommend reusing soil directly for new microgreen grows. Microgreens grow so densely that any pathogens in used soil can multiply quickly and ruin a tray. Compost the used soil first and use the finished compost in outdoor gardens. Start microgreens with fresh, clean medium every time.
How do you clean reusable microgreen grow mediums?
Remove the root mat with our Microgreen Medium Scraper, rinse with running water, wash with free-and-clear dish soap using your hands (no brushes), then sanitize by boiling for 1 to 2 minutes, soaking in hot soapy water for 20 minutes, or spraying with 3% hydrogen peroxide for 10 to 20 minutes. The silicone is also dishwasher safe (top rack, no heat). Air dry completely before storing.
How long does a reusable silicone grow medium last?
Our 1.2mm reusable silicone grow medium is rated for 20 to 30+ growing cycles under normal conditions, or roughly 18 to 24 months of regular use with proper care. Cosmetic staining from red or pigmented seeds doesn't affect performance. Replace when you see tears, cuts, loss of flexibility, or surface degradation.
Can microgreen leftovers go in a regular compost bin?
Yes. Microgreen root mats are perfect compost material. They count as "green" (nitrogen-rich) compost material because of the fresh plant tissue. Just mix them in with your other compost materials and let the bin do its work. The mix of soil (or coco coir) and plant matter actually accelerates the breakdown process for the rest of your compost.
Can I compost coco coir from microgreens?
Yes. Coco coir is fully compostable, though it breaks down slightly slower than soil. You can compost it in a backyard bin, use it directly as a soil amendment in outdoor garden beds, or use it as mulch around outdoor plants. We don't recommend trying to clean and reuse coco coir for new microgreen grows since the roots tangle into the fibers and separation is tedious.
What about composting Biostrate or other special mats?
Biostrate requires industrial composting facilities to break down properly. Standard backyard bins don't generate enough heat. Check if your area has industrial composting that accepts it. Hemp, jute, and other plant-based mats can go straight in a backyard bin, but Biostrate typically needs commercial facilities or has to go in the trash.
Is composting microgreen waste better than throwing it away?
Yes, significantly. Organic waste in landfills breaks down without oxygen and releases methane (a greenhouse gas roughly 25 times more potent than CO2). Composting breaks down the same material aerobically into nutrient-rich soil amendment that benefits your garden. From an environmental standpoint, composting is dramatically better.
Can I use leftover compost from microgreens to grow more microgreens?
We don't recommend it. Compost from microgreen leftovers can carry pathogens that thrive in the dense, humid conditions of microgreen production. Use that compost in outdoor garden beds where pathogens are less likely to cause problems and the broader soil ecosystem keeps things in balance. Start microgreens with fresh, clean medium every grow.
How can I reduce waste from growing microgreens?
The single most effective way to reduce microgreen growing waste is to switch to a reusable silicone grow medium. After the initial investment, your only "waste" is the organic root mat, which composts quickly. Our 7x14 OTG Microgreen Tray Kit includes two reusable silicone grow mediums and is the easiest way for home growers to get started with a zero-medium-waste setup.
Final Thoughts
Cleanup and disposal might not be the most exciting part of growing microgreens, but having efficient systems in place makes it quick and painless. The method that works best for you depends on your growing medium, available space, local resources, and personal priorities.
For most home growers, we recommend keeping it simple: compost disposable mediums, or invest in a quality reusable silicone grow medium that lasts for years. Don't overthink it. The few minutes spent on proper disposal and cleanup ensure your next grow starts fresh and clean.
And hey, there's something satisfying about knowing that this week's harvest leftovers will become next season's garden soil. It's the circle of life, microgreen edition.
Happy growing (and happy composting)! 🌱
-CJ & Mandi
Related Blogs You Might Enjoy
- How to Start Growing Microgreens: A Beginner's Guide
- How to Grow Broccoli Microgreens
- How to Water Microgreens: The Complete Watering Guide
- How to Clean and Sanitize Microgreen Trays and Reusable Mediums
- Meet Our Reusable Silicone Grow Medium
- Which Microgreen Seeds Work on Reusable Grow Mediums?
- Why We Don't Eat Microgreen Roots Like Sprouts
- Why Are My Microgreens Moldy? Mold vs. Root Hairs Guide
- Top Microgreen Growing Mistakes and How to Avoid Them
- Case Study: Coco Coir vs. Reusable Grow Medium
- Best Microgreen Growing Advice and Resources
Published: January 2020
Updated: May 23, 2026
All content is property of On The Grow®, LLC
Where can you get your sprayer??