You've harvested your microgreens, but you're left with a tray containing growing medium, roots, seed hulls and hundreds of short cut stems.
What should you do with it?
Can you simply sow another crop into the same soil or coco coir?
For most home growers, the better approach is to remove the old root mat, compost or repurpose suitable material, clean the tray and start the next microgreen crop with fresh growing medium.
Used microgreen medium doesn't necessarily need to go to waste. Depending on what you've grown in and the condition of the crop, it can often be composted or repurposed elsewhere in the garden.
This guide explains your options.
Used Microgreen Medium: Quick Guide
| Growing Medium | Sow Microgreens Straight Into It Again? | Compost? | Best Next Step |
|---|---|---|---|
| Seed-raising mix | Generally not recommended | Usually yes | Compost or repurpose in garden |
| Coco coir | Generally not recommended without processing | Usually yes | Compost or mix into garden material |
| Coco/soil blends | Generally not recommended | Usually yes | Compost or repurpose |
| Biodegradable growing mats | Depends on material | Often | Check manufacturer instructions |
| Synthetic growing mats | No | No | Clean/reuse if designed for it or dispose appropriately |
| Medium from mouldy/spoiled crop | No | Depends on circumstances | Keep away from new microgreen crop |
Why Is There Such a Dense Root Mat?
Microgreens are grown at much higher densities than mature garden plants.
A tray may contain hundreds or even thousands of seedlings growing close together.
By harvest time, their roots have often formed a dense network throughout the growing medium.
When you lift the crop from the tray, the entire contents may come out as one solid mat containing:
-
Roots
-
Growing medium
-
Seed hulls
-
Ungerminated seeds
-
Short cut stems
-
Other plant material
That's completely normal.
A healthy root mat is a sign that the seedlings have established throughout the growing medium.
Can You Reuse Microgreen Soil?
Technically, used soil or seed-raising mix can be processed and reused, but sowing another dense microgreen crop directly into the freshly harvested root mat isn't generally recommended.
The old medium now contains:
-
A dense network of roots
-
Cut plant stems
-
Seed remains
-
Decomposing organic material
-
Areas where the structure has changed
-
Nutrients already used by the previous crop
Trying to sow another dense crop directly on top can produce a less predictable growing environment.
For home growers, starting with fresh suitable growing medium is usually simpler and more reliable.
Can You Reuse Coco Coir for Microgreens?
Coco coir is reusable in some gardening applications, but the same issue applies.
After a microgreen crop, the coir is normally tightly bound together by thousands of roots.
Simply cutting the crop and sprinkling another layer of seed on top isn't the same as starting with fresh coir.
To reuse it for another microgreen crop, you would need to:
-
Remove substantial root material
-
Break the coir apart
-
Assess its condition
-
Deal with remaining plant debris
-
Consider sanitation
-
Restore an appropriate moisture level and structure
For a small home tray, the time and effort involved often outweigh the value of the coir recovered.
Composting or repurposing it elsewhere is generally easier.
Why Not Just Pull Out the Roots?
Microgreen roots aren't like pulling one tomato plant from a garden bed.
Because microgreens are densely sown, their fine roots become intertwined throughout the growing medium.
Removing every root while retaining clean, loose growing medium can be surprisingly difficult.
You can certainly break the root mat apart, but at that point the material is often more useful as compost input or garden organic material than as a pristine medium for another dense microgreen sowing.
What About Reusing Only the Loose Growing Medium?
Sometimes loose material remains around the edges or underneath the main root mat.
If it is clean and free from obvious plant debris, it can potentially be repurposed elsewhere.
However, for your next microgreen tray, we still recommend starting with fresh growing medium.
Microgreens have a short growing cycle, and a clean, consistent starting medium makes watering, germination and root development more predictable.
For information about choosing growing media, see Best Growing Medium for Microgreens: Coco Coir, Seed-Raising Mix & Mats.
Can You Compost Used Microgreen Growing Medium?
In many cases, yes.
A healthy harvested microgreen root mat can make useful compost material.
Depending on what you used, the mat may contain biodegradable materials such as:
-
Plant roots
-
Cut stems
-
Seed hulls
-
Coco coir
-
Seed-raising mix
-
Other organic growing material
Rather than putting the entire dense mat into your compost intact, breaking it into smaller pieces can help it mix with the other compost ingredients.
How to Compost a Microgreen Root Mat
A simple approach is:
-
Remove the root mat from the tray.
-
Break or tear it into smaller pieces.
-
Add it to your compost.
-
Mix it with the existing compost materials.
-
Continue managing your compost normally.
The dense root network will break down over time along with the other plant material.
If the mat is extremely wet, allowing excess moisture to drain before adding it can make handling easier.
Can Used Microgreen Medium Go Into a Worm Farm?
Suitable untreated organic material may be appropriate for some worm farms, but don't overwhelm the system with large quantities at once.
A dense microgreen root mat can contain a considerable amount of organic material.
Break it into smaller pieces and introduce modest amounts alongside the other materials you normally feed your worm farm.
Whether a particular growing mat or other medium is suitable depends on what it is made from.
Don't put synthetic growing media into a worm farm.
Can You Put Used Coco Coir in the Garden?
Yes, suitable used coco coir can often be repurposed as organic material in the garden.
After removing or breaking up the root mat, it can be incorporated into:
-
Compost
-
Garden beds
-
Potting-medium blends
-
Other suitable garden applications
Coco coir helps hold moisture, but remember that used coir from a microgreen tray also contains old roots and other crop residue.
Think of it as a garden amendment or compost ingredient, rather than fresh sterile growing medium.
Can Used Seed-Raising Mix Go Into the Garden?
Generally, healthy used seed-raising mix can also be repurposed.
You might:
-
Add it to compost.
-
Mix small amounts into garden soil.
-
Use it as part of a larger garden-bed amendment.
-
Incorporate it into other suitable outdoor growing areas.
The exact approach depends on what the original mix contains and what you intend to grow next.
Again, this is different from recommending that the same material be immediately used for another dense tray of edible microgreens.
What About Biodegradable Microgreen Mats?
It depends on the mat.
Growing mats can be made from materials such as:
-
Hemp
-
Jute
-
Coco fibre
-
Wood fibre
-
Other plant-based fibres
Some are biodegradable or compostable.
Others may contain binders, backing materials or synthetic components.
Check the manufacturer's instructions before putting a growing mat into home compost.
Don't assume a product is compostable simply because it looks like natural fibre.
What About Synthetic Growing Mats?
Synthetic mats shouldn't be added to compost.
If a synthetic mat is designed to be reusable, clean it according to the manufacturer's instructions before using it again.
If it is a single-use product, dispose of it according to the appropriate local waste guidance.
This is one reason reusable trays combined with compostable growing media can be attractive for home growers wanting to reduce waste.
Should You Sterilise Used Growing Medium?
For most home microgreen growers, attempting to sterilise old soil or coco coir solely so it can be used for another tray usually isn't worth the effort.
Properly treating growing medium can involve:
-
Removing roots and plant material
-
Breaking up the medium
-
Heat or other treatment
-
Reconditioning moisture
-
Restoring structure
-
Potentially restoring nutrients
Even after all that, the result may still be less consistent than starting with fresh medium.
Commercial growers may make different decisions based on scale and economics.
For a home tray, composting or repurposing the old material is usually the simpler option.
What if the Previous Crop Had Mould?
Treat growing medium from a mouldy or badly deteriorated crop differently from a healthy harvested root mat.
Don't sow another microgreen crop directly into it.
Remove the affected crop and medium from the tray.
If you maintain a home compost system, whether diseased or mould-affected plant material belongs in it depends on the nature of the problem and how your compost is managed. A well-managed hot compost system behaves differently from a small cool compost pile.
If you're uncertain about what affected the crop, keeping questionable material away from future edible seedling production is the conservative approach.
Most importantly, don't transfer the old medium directly into your next microgreen tray.
Mould or Root Hairs?
Before discarding a crop because you think it has mould, make sure you're identifying it correctly.
Microgreen roots can develop fine white root hairs, particularly when searching for moisture.
These can look remarkably like mould.
Root hairs are part of normal plant growth.
If you're unsure, see our Mould vs Root Hairs on Sprouts & Microgreens guide.
Clean the Tray Before Starting Again
Once you've removed the old root mat and growing medium, don't immediately refill the dirty tray.
Remove:
-
Roots
-
Seed hulls
-
Growing-medium residue
-
Cut stems
-
Other plant debris
Then wash the tray thoroughly.
Starting each crop in a clean tray helps prevent old plant material from carrying over into the new growing cycle.
For the complete cleaning method, see How to Clean & Sanitise Sprouting Jars and Microgreen Trays.
Do You Need Fresh Growing Medium for Every Crop?
For reliable home microgreen production, fresh growing medium is generally the simplest approach when using soil, seed-raising mix or coco coir.
That doesn't mean the old material must be thrown into general waste.
The better cycle is often:
Grow microgreens → harvest → compost or repurpose the old medium → clean the tray → add fresh medium → sow again.
This allows the tray itself to be reused repeatedly while the organic growing material returns to another useful purpose.
How Can You Reduce Waste When Growing Microgreens?
Home microgreen growing doesn't need to produce large amounts of waste.
A few simple practices help:
Use Reusable Trays
Good-quality growing trays can be washed and used repeatedly.
Compost Suitable Growing Medium
Healthy root mats, coco coir and suitable organic growing mixes can often become compost material instead of rubbish.
Choose Growing Media Carefully
If compostability matters to you, check what a growing mat or medium actually contains before buying it.
Grow the Right Amount
Sowing more trays than you can eat wastes seed, growing medium, water and the finished crop.
Match production to what your household actually uses.
Harvest Properly
A clean harvest leaves less loose plant material scattered through the tray and makes cleanup easier.
For harvesting guidance, see How to Harvest & Store Microgreens.
What if You Want a Second Harvest?
Before removing the root mat, consider whether the crop is one that can produce useful regrowth.
Pea shoots are one of the better examples, and wheatgrass can also produce additional growth.
Most common microgreens are better treated as single-harvest crops.
If you want to attempt another harvest, see Can Microgreens Regrow After Cutting? before clearing the tray.
Frequently Asked Questions
Can you reuse microgreen soil?
It can be repurposed, but sowing another dense microgreen crop directly into the freshly harvested root mat isn't generally recommended.
Composting or using healthy spent medium elsewhere in the garden is usually more practical.
Can you reuse coco coir after growing microgreens?
Coco coir can be reused in other gardening applications, but after a microgreen crop it is normally filled with dense roots and plant residue.
For the next microgreen crop, starting with fresh coir is generally simpler.
Can I plant another microgreen crop on top of the old roots?
We don't recommend it.
Remove the old root mat, clean the tray and start again with fresh suitable growing medium.
Can microgreen root mats be composted?
Healthy root mats made from plant material and suitable organic growing medium can generally be composted.
Break dense mats into smaller pieces to help them mix with the rest of your compost.
Can coco coir go into compost?
Yes, suitable untreated coco coir can be incorporated into compost.
Mix it with other compost materials rather than relying on large quantities of coir alone.
Can I put used microgreen soil in my garden?
Healthy used growing medium can often be repurposed in garden beds or compost, depending on what the original medium contains.
Should I sterilise old microgreen soil?
For most home growers, processing and sterilising old medium specifically for another microgreen crop isn't worth the effort.
Fresh medium provides a cleaner and more predictable starting point.
What should I do with a mouldy microgreen root mat?
Don't reuse it for another microgreen crop.
Remove it from the tray, clean the tray thoroughly and use fresh growing medium for the next crop.
Can I compost a microgreen growing mat?
Only if the manufacturer identifies the material as suitable for composting.
Some natural-fibre mats are biodegradable, while others contain synthetic components or binders.
Complete the Microgreen Growing Cycle
Harvesting isn't quite the end of a microgreen crop.
Once you've finished with the tray:
Consider regrowth → remove the root mat → compost or repurpose suitable material → clean the tray → add fresh growing medium → sow the next crop.
For most home growers, we recommend fresh growing medium for each new microgreen crop rather than sowing directly into an old root mat.
The spent material can still have another useful life in compost or the garden.
For help choosing your next medium, see Best Growing Medium for Microgreens: Coco Coir, Seed-Raising Mix & Mats.
For cleaning your equipment before the next crop, see How to Clean & Sanitise Sprouting Jars and Microgreen Trays.
And for the complete growing process, see How to Grow Microgreens at Home in Australia.
Browse the OzSprout Microgreen Seeds range when you're ready to start your next tray.