How to Clean & Sanitise Sprouting Jars and Microgreen Trays

Clean growing equipment is an important part of successfully growing sprouts and microgreens at home.

Sprouting jars stay moist for several days, while microgreen trays can collect roots, seed hulls and growing-medium residue after harvest. Simply rinsing the equipment and putting it away isn't always enough.

A good routine is straightforward:

Remove debris → wash → rinse → sanitise when appropriate → air dry completely.

This guide explains how to clean sprouting jars, sprouting lids and microgreen trays between crops, when sanitising is useful and how to store your equipment ready for the next grow.

Cleaning vs Sanitising: What's the Difference?

Cleaning and sanitising aren't the same thing.

Cleaning

Cleaning physically removes:

• Seed hulls

• Roots

• Coco coir and other growing-medium residue

• Dirt

• Organic matter

• Other visible residue

For home growing equipment, this generally means washing thoroughly with warm to hot water and detergent, using physical action where necessary, then rinsing.

Sanitising

Sanitising is an additional step performed after cleaning to reduce microorganisms remaining on a clean surface.

This distinction matters.

A sanitiser won't work as effectively if roots, soil, coco coir, seed residue or detergent are still covering the surface.

Always clean first. Sanitise second.

Do Sprouting Jars and Microgreen Trays Need to Be Sanitised After Every Crop?

At a minimum, growing equipment should be thoroughly cleaned and dried between crops.

Sanitising provides an additional hygiene step and is particularly worthwhile for equipment that comes into direct contact with seeds, sprouts, roots or harvested food.

It is especially sensible to sanitise when:

• Starting a new crop

• Equipment has been stored for a long period

• There is stubborn organic residue

• A previous crop deteriorated

• There has been suspected contamination

• Equipment has been handled or stored somewhere unclean

If a previous crop developed obvious mould or spoilage, thoroughly clean and sanitise the equipment before using it again.

How to Clean a Sprouting Jar

A glass sprouting jar is relatively easy to clean, but pay attention to the rim, threads and any areas where seed hulls can become trapped.

Step 1: Empty the Jar Completely

Remove all remaining:

• Sprouts

• Seeds

• Roots

• Seed hulls

• Other debris

Don't wash large quantities of seed or root material down the sink if they can easily be removed first.

Step 2: Rinse

Rinse the jar to remove loose material.

Pay particular attention to the bottom corners and around the threaded opening.

Step 3: Wash With Detergent

Wash the jar thoroughly using warm to hot water and normal dishwashing detergent.

Use a clean dish brush, bottle brush or sponge to reach the entire inside surface.

Clean:

• Inside the jar

• Outside the jar

• Rim

• Threads

• Base

Visible residue should be completely removed.

Step 4: Rinse Thoroughly

Rinse away the detergent and any remaining loosened material with clean water.

The jar should now be visibly clean before moving on to sanitising.

Step 5: Sanitise if Required

Use one of the suitable sanitising methods described below.

Step 6: Air Dry

Allow the jar to air dry completely.

Store it somewhere clean and dry until you're ready to grow another batch.

How to Clean a Sprouting Lid

Sprouting lids deserve extra attention because their mesh, perforations and threads can trap small seeds and seed hulls.

After every crop:

1. Remove the lid from the jar.

2. Rinse away loose seeds and hulls.

3. Wash thoroughly with warm to hot water and detergent.

4. Use a clean brush to remove material caught in the mesh or perforations.

5. Rinse thoroughly.

6. Sanitise when appropriate.

7. Allow the lid to air dry completely.

Hold mesh lids up to the light after washing. If you can still see material trapped in the mesh, clean them again before storage.

If your sprouting lid contains several removable components, separate them where the manufacturer's design allows so all surfaces can be reached.

How to Clean Microgreen Trays After Harvest

Microgreen trays usually require more physical cleaning than sprouting jars because roots and growing medium can remain attached after harvest.

Step 1: Remove the Root Mat

After harvesting, lift out as much of the root mat and growing medium as possible.

Most of the material should be removed before the tray reaches the sink.

If you compost at home, suitable plant and growing-medium waste can be added to your compost according to your normal composting practices.

Step 2: Remove Loose Material

Shake, brush or scrape away loose:

• Roots

• Coco coir

• Seed-raising mix

• Seed hulls

• Plant material

Pay particular attention to drainage holes and corners.

Step 3: Rinse the Tray

Rinse away the remaining loose residue.

For trays with drainage holes, rinse both sides because roots can become lodged in the openings.

Step 4: Wash With Detergent

Wash the tray with warm to hot water and detergent.

Use a brush or sponge to clean:

• Growing surface

• Corners

• Side walls

• Underside

• Drainage holes

• Ridges and channels

If residue has dried onto the tray, soaking it first can make removal easier.

Step 5: Rinse

Rinse thoroughly to remove detergent and loosened debris.

Inspect the tray before sanitising.

If you can still see growing-medium residue or plant material, clean it again.

Step 6: Sanitise

Once the tray is visibly clean, sanitise it using an appropriate method.

Step 7: Air Dry Completely

Allow the tray to dry completely before stacking or storing it.

Don't stack damp trays tightly together for storage.

Trapped moisture between trays creates exactly the type of damp environment you're trying to avoid.

How to Sanitise Sprouting and Microgreen Equipment

There are several ways to sanitise clean food-contact equipment.

The appropriate method depends on the material and the equipment manufacturer's instructions.

Option 1: Use a Food-Safe Commercial Sanitiser

For most home growers wanting a chemical sanitising method, a commercial sanitiser specifically labelled as suitable for food-contact surfaces or equipment is the simplest approach.

Different products have different:

• Dilution rates

• Contact times

• Water-temperature requirements

• Rinsing requirements

Always follow the product label.

Don't assume that using more sanitiser makes it more effective. The correct concentration and contact time are important.

The general process is:

1. Clean the equipment thoroughly.

2. Rinse away detergent.

3. Prepare or apply the sanitiser exactly as directed.

4. Ensure the sanitiser contacts all relevant surfaces.

5. Leave it in contact for the specified time.

6. Rinse afterward if the product instructions require it.

7. Allow the equipment to air dry.

Only use a product suitable for the material you're cleaning.

Option 2: Use Heat

Heat can also be used to sanitise suitable equipment.

Food-safety guidance recognises immersion in very hot water as a sanitising method.

However, not all home-growing equipment is suitable for very hot water.

Glass, plastics, seals and other components can have different temperature limitations.

Before using very hot water:

• Check the equipment manufacturer's instructions.

• Make sure the material is heat-safe.

• Avoid sudden temperature changes with glass.

• Don't expose plastic trays or lids to temperatures that may warp or damage them.

For suitable equipment, current Australian food-safety guidance uses 77°C for at least 30 seconds as a hot-water sanitising method.

Option 3: Use a Dishwasher

A dishwasher can be useful for equipment that the manufacturer confirms is dishwasher-safe.

Before putting sprouting or microgreen equipment into a dishwasher:

• Check that the item is dishwasher-safe.

• Remove seeds, roots and growing-medium residue first.

• Make sure water can reach all surfaces.

• Secure small components so they don't fall through racks or interfere with the dishwasher.

• Use the appropriate cycle for the item.

Where sanitising is the objective, use the dishwasher's longest, hottest suitable cycle or sanitation program.

Check that equipment is clean when the cycle finishes and allow it to dry thoroughly.

Don't put equipment into a dishwasher simply because it fits. Some plastics, seals and other components may be damaged by high temperatures.

What About Bleach?

Plain unscented bleach can be used as a sanitiser when it is correctly diluted and used according to appropriate food-safety instructions.

However, bleach products vary considerably in chlorine concentration.

That means a universal instruction such as "add one capful to a bucket" isn't reliable.

If you choose to use bleach:

• Use plain, unscented bleach.

• Check its chlorine concentration.

• Follow current food-safety guidance and the manufacturer's instructions.

• Use the correct dilution.

• Observe the required contact time.

• Follow any rinsing instructions.

• Never mix bleach with other cleaning chemicals.

For most home growers, a commercial food-contact sanitiser with clear label instructions can be simpler than calculating bleach concentrations.

Does Vinegar Sanitise Sprouting Jars and Trays?

Vinegar is commonly recommended online as a natural cleaning product, but it shouldn't automatically be treated as a substitute for a validated food-contact sanitiser.

Vinegar can be useful for some general cleaning tasks and removing certain mineral deposits, but if your objective is sanitising food-contact growing equipment, use a recognised sanitising method.

That could include:

• A suitable food-contact sanitiser

• An appropriate hot-water method

• A suitable dishwasher sanitising cycle

The fact that something is natural doesn't necessarily mean it provides a reliable sanitising process.

Should You Sanitise Before or After Cleaning?

Always clean first.

The correct order is:

1. Remove debris
2. Rinse
3. Wash with detergent
4. Rinse away detergent
5. Sanitise
6. Air dry

This is one of the most important points in this guide.

Sanitiser isn't designed to replace proper cleaning.

Roots, seed hulls, growing medium and other organic matter need to be physically removed first.

What Should You Do After a Mouldy or Spoiled Crop?

If a crop develops obvious mould or spoilage, don't simply empty the equipment and immediately start another crop.

Instead:

1. Discard the affected crop.

2. Remove all seeds, roots and growing material.

3. Rinse away loose debris.

4. Wash the equipment thoroughly with detergent.

5. Rinse completely.

6. Sanitise using an appropriate method.

7. Allow everything to air dry completely.

8. Inspect the equipment before using it again.

Pay particular attention to:

• Mesh

• Drainage holes

• Corners

• Threads

• Seams

• Ridges

• Other areas where organic material can remain trapped

If you aren't sure whether you're seeing mould or normal root development, see our Mould vs Root Hairs on Sprouts & Microgreens guide.

Why Air Drying Matters

Cleaning doesn't finish when you put down the brush.

Equipment should also be thoroughly dried before storage.

Air drying is preferable because reusable tea towels can potentially transfer material back onto freshly cleaned equipment.

Place jars, lids and trays somewhere clean with good airflow and allow them to dry completely.

Don't put a lid onto a damp jar and store it sealed.

Don't tightly stack wet microgreen trays.

Allow moisture to escape before putting equipment away.

How to Store Clean Growing Equipment

Once completely dry:

• Store jars somewhere clean and protected from dust.

• Keep sprouting lids dry.

• Store trays in a clean, dry area.

• Avoid hot, damp sheds or other unsuitable locations.

• Don't store clean growing equipment alongside garden chemicals or other potential contaminants.

If equipment has been stored uncovered for a long period, wash it again before use.

When Should Growing Equipment Be Replaced?

Reusable growing equipment can last a long time when properly maintained, but it should still be inspected regularly.

Consider replacing an item if it develops:

• Deep scratches that are difficult to clean

• Cracks

• Broken mesh

• Damaged drainage holes

• Persistent residue that cannot be removed

• Corrosion

• Warping

• Damaged surfaces that can no longer be cleaned effectively

A smooth, intact surface is much easier to clean than a heavily damaged one.

Glass jars should be discarded if they are cracked or chipped.

Cleaning Before Your First Grow

New equipment should also be cleaned before its first use.

Manufacturing, packaging, storage and handling can leave dust or other residues on a product before it reaches your kitchen.

Before the first crop:

1. Wash the equipment with warm to hot water and detergent.

2. Rinse thoroughly.

3. Sanitise food-contact equipment if appropriate.

4. Allow it to air dry or use it immediately with clean hands.

Starting with clean equipment gives your first crop the same preparation as every crop that follows.

Keep Your Hands Clean Too

Clean equipment only helps if it remains clean while you're using it.

Before handling seeds, sprouts or freshly cleaned equipment:

• Wash your hands thoroughly with soap and water.

• Dry them with a clean towel.

• Avoid handling sprouts immediately after touching raw meat, pets, rubbish or other potential sources of contamination without washing your hands again.

Try to handle the sprouts themselves only when necessary.

Frequently Asked Questions

Do I need to clean my sprouting jar after every batch?

Yes.

Wash the jar and lid thoroughly after every batch, remove all seed and plant residue, rinse and allow the equipment to dry.

Sanitising provides an additional hygiene step and is particularly useful before starting a new crop and after any suspected contamination or spoilage.

Can I wash a sprouting jar with normal dishwashing liquid?

Yes.

Warm to hot water and normal dishwashing detergent can be used for the cleaning stage.

Rinse thoroughly afterward so detergent residue is removed.

Can sprouting jars go in the dishwasher?

Many glass jars can, but the lid and other components may have different requirements.

Check the manufacturer's instructions for your particular equipment.

Can microgreen trays go in the dishwasher?

Some can and some cannot.

High temperatures may warp certain plastics, so check the tray manufacturer's instructions before using a dishwasher.

Should I sanitise dirty equipment without washing it first?

No.

Remove debris and wash the equipment first.

Sanitising works on an already clean surface and shouldn't be used as a shortcut around proper cleaning.

Can I use vinegar instead of sanitiser?

Don't assume vinegar provides the same sanitising performance as a product or heat process intended for food-contact sanitising.

If sanitising is required, use a recognised food-contact sanitising method.

Can I use bleach?

Plain unscented bleach can be used when correctly diluted, but bleach products vary in strength.

Follow the product instructions and current food-safety guidance rather than guessing the dilution.

Never mix bleach with other cleaning chemicals.

Why should microgreen trays be completely dry before stacking?

Stacking wet trays can trap moisture between them.

Allowing trays to air dry completely before storage helps keep the equipment clean and ready for the next crop.

What should I do if my previous crop had mould?

Discard the crop, thoroughly remove all organic material, wash the equipment, rinse, sanitise and allow it to dry completely before starting again.

A Simple Cleaning Routine to Remember

You don't need a complicated cleaning system for home sprouting and microgreen growing.

Remember:

REMOVE → WASH → RINSE → SANITISE → AIR DRY

Remove roots, seeds and growing medium.

Wash thoroughly with detergent.

Rinse away detergent and loosened debris.

Sanitise clean food-contact equipment using an appropriate method.

Allow everything to air dry completely before storage.

Clean equipment won't guarantee that every crop succeeds, but it removes one major source of avoidable growing and food-safety problems.

If you're growing sprouts, see our How to Grow Sprouts in a Jar guide and Sprouting Seed Guide: Soak Times, Quantities & Harvest Times.

For microgreens, see How to Grow Microgreens at Home in Australia for the complete growing process.

Browse Sprouting Jars & Equipment for equipment designed for home sprouting and growing.