What To Do With Microgreens After Harvest: Your Complete Guide to Cleanup and Disposal
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.
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.
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 situation. 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 2-10 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.
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.
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 Grow Mediums: Cleaning and Sanitizing for Next Use
If you're using our Stainless-Steel Reusable Grow Medium or Silicone Reusable Grow Medium, the cleanup process is different—but that's the whole point of reusable mediums! Instead of disposal, you're cleaning for the next grow.
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/Cleaner 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 medium under running water, remove any remaining debris. The goal is to remove all organic material completely. Then you will wash it with a free and clear dish soap and rinse.
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.
For Silicone Reusable Grow Medium: Boiling water is your best option. Submerge the silicone sheets in boiling water for 1-2 minutes. This effectively kills bacteria, fungi, and other pathogens. Let air dry completely before your next use.
For Stainless-Steel Reusable Grow Medium: You can use boiling water (though be careful handling hot steel), or use hydrogen peroxide. Spray or wipe the entire surface with 3% hydrogen peroxide solution and let air dry. No rinsing needed.
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.
For complete details on cleaning reusable mediums, check out our comprehensive guides:
How Long Do Reusable Mediums Last?
With proper cleaning and sanitization, our reusable grow mediums last for months. We have growers using the same stainless-steel sheets for many grows without issues. 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 180-200°F (82-93°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 Stainless-Steel or Silicone Reusable Grow Mediums are 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.
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 and stainless-steel): These are 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.
Common Questions About Microgreen Disposal
"Can I use my finished root mat compost for growing microgreens again?"
We don't recommend it. Use finished compost from microgreen leftovers in outdoor gardens only. The risk of pathogen buildup is too high for the controlled environment of microgreen production. Microgreens grow so quickly and densely that any disease issues spread rapidly, and using potentially contaminated medium isn't worth the risk.
"What if my tray had mold—can I still compost it?"
For backyard composting, a moldy tray going into your compost isn't a big concern—the composting process will break everything down. However, keep moldy material away from healthy growing areas until it's in the compost bin. And always sanitize any trays that held moldy crops before using them again.
"How can I make disposal easier and faster?"
The key is having systems in place. Keep a small compost bucket near your growing area for quick root mat disposal. Clean and sanitize trays immediately after disposing of the root mat—don't let them sit around getting crusty and harder to clean. If using reusable mediums, clean them right away while everything is still fresh.
"Is there any way to reduce waste in the first place?"
Yes! Using reusable grow mediums is the most effective way to reduce waste. Our 7x14 OTG Microgreen Tray Kit, Large Sprouting Tray Set, and Small Sprouting Tray Set all include reusable silicone grow mediums. After the initial purchase, your only "waste" is the organic plant material (roots and stems), which composts quickly.
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 quality reusable mediums that last 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)! 🌱
Published: January 2026
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