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When I noticed the walls of my greenhouse covered in a thin layer of grime last week, I realized it was time to take action. Those filthy windows were blocking precious sunlight from reaching my plants. But polycarbonate requires special care to prevent damage. After some research & trying a few things out, here’s what I’ve learned about keeping a polycarbonate greenhouse clean.

To keep your polycarbonate greenhouse clean, wash the glazing with soapy water & a soft sponge. Never use ammonia- or alcohol-based cleaning products, since they can damage polycarbonate. Never use a dry cloth, since polycarbonate scratches very easily. Prevent future grime, pests, & diseases via lower humidity to minimize condensation.


As straightforward as this process is, there are few things that you’ll want to keep in mind. Polycarbonate differs from other greenhouse glazing materials, so you have to make sure that you’re using a cleaning solution that won’t damage it.

Polycarbonate vs. other materials

To start off, it’s helpful to know the difference between polycarbonate greenhouses and glass or other glazing materials.

Using the wrong cleaning agent on your greenhouse could cause irreversible damage, so it’s worth paying attention to what you’re using.

Polycarbonate is a special type of plastic. It’s extremely strong and resistant to breaking–roughly 250 times stronger than glass. Holy moly!

But, polycarbonate will scratch very easily. So, never wipe down polycarbonate with a dry cloth, since the dust & dirt particles act as knives, etching the glazing.

IMPORTANT: In addition, below in this article I mention cleaning for the greenhouse structure/framing, pots & trays, irrigation & hoses, etc. Cleaning for those elements may require an oxygen bleach solution–to sterilize & remove disease. But, on polycarbonate, you should ONLY use dishsoap or a solution specifically for polycarbonate, since you don’t want to damage the polycarbonate.

One of the best aspects about polycarbonate is its insulation. Plastic has better heat retention properties than glass and will keep your greenhouse warmer at a lower price. While a single sheet of polycarbonate won’t be as effective as glass, most polycarbonate building materials for greenhouse are double-walled. Two sheets of polycarbonate are put together with a space in between to allow for increased heat retention.

Polycarbonate also lasts longer than glass, and in the unfortunate occasion that it does become damaged, it’s much easier to replace.

Besides all of the benefits that come with it being easier to work with, polycarbonate sheets also provide better light diffusion than glass. This is a huge benefit as the plants inside will receive an equal amount of sunlight and maximize their growth potential.

Polycarbonate sheets are also treated with an ultraviolet resistant coating on one side that protects both the plants and the longevity of the structure.

POlycarbonate Glass
Cost More expensive Less expensive
Insulation Better heat retention Relatively poor insulation
Light Diffused light

UV coating available

Direct light
Durability Extremely strong

Can scratch easily

Can shatter easily

Extremely scratch resistant

Why should you clean a greenhouse?

In order to maximize the productivity and health of your greenhouse, it’s essential to stay on top of cleaning it.

Without regular maintenance, your plants are much more susceptible to unwanted pests and diseases.

While a greenhouse provides the perfect environment to protect plants from harsh weather, it can also provide the ideal climate for unwanted pests. Tiny insects will thrive wherever you give them a chance, so regularly cleaning is essential. Gnats, for example, will reproduce on organic residues.

Pests and pathogens can live in not only the plant material, but on the polycarbonate walls as well. Giving the polycarbonate sheets a thorough cleaning helps to prevent algae and mold from forming.

Just a little maintenance can go a long way in making sure that your plants thrive. Learn from my mistakes and clean your greenhouse before it’s needed, it pays off in the long run.

Disinfecting your greenhouse gives both your plants and the structure itself the best possible chance to thrive. Knowing how to identify pests and diseases in your greenhouse is essential to keeping it healthy.

How often should you clean a greenhouse?

If you want to avoid letting your greenhouse get filthy (like I did…), there are a few things that you should do to maintain it.

Regularly wash the windows of your greenhouse to prevent them from getting dirty and blocking the light that your plants need. Pay attention to any buildup or grime on the windows and attend to it as you go.

Regularly sweep the floor and remove dead plant materials like leaves.

Once a year, you should remove everything from your greenhouse and clean the whole thing. Yes, this can be a daunting process if you have a large greenhouse, but it’s worth the wellbeing of your plants. If you do this during the wintertime, make sure to put your plants in an area where they won’t freeze, like the garage.

Take this time to thoroughly disinfect the structure of your greenhouse.

This not only improves the longevity of your greenhouse and allows you to identify any problems before they become issues, but also provides your plants with a safe and healthy environment to grow in.

What should you use to clean a greenhouse?

Cleaning the polycarbonate walls of your greenhouse doesn’t require any fancy solutions. In fact, the easiest and safest way to clean them is with a mild soap such as dish-washing liquid. This is what I recommend as most other household cleaning products contain at least one chemical that can damage the coating on your polycarbonate panels.

Also make sure to you use a non-abrasive sponge as to not damage the material.

If you have wood framing, you’ll want to treat it as well. The last thing you want is wood rot in your framing–it’s super expensive to repair. To treat wood framing, use a non-toxic vegetable-based horticultural oil.

Metal frames can simply be wiped down with your chosen disinfectant.

To reiterate, here’s what you’ll need:

  • A broom
  • A non-abrasive sponge
  • dishsoap or a polycarbonate-specific cleaner
  • A vegetable-based horticultural oil (if the frame is made of wood)

How should you clean your greenhouse?

Now that you know which solutions are safe to use while cleaning your polycarbonate greenhouse, here’s how to go about it.

Polycarbonate sheets 

If you skipped down to this section, I need to reiterate a super-important point: Polycarbonate can scratch VERY easily, and common household cleaners WILL damage it.


  • Use ONLY dishsoap or a polycarbonate-specific cleaning solution.
  • NEVER use a dry cloth to wipe down polycarbonate. The tiny dust & dirt grains with carve scratches into the pane.

Mix a few drops of dishsoap in a one gallon bucket of water. Gently wash the inside of the polycarbonate sheets to loosen any dirt and grime buildup.

Rinse down the walls with a hose and proceed to dry them with a fresh towel to avoid water spots.

For the outside of the sheets, simply rinsing them down with a hose should do the trick. If you notice that the panels are still dirty, use the cleaning solution and sponge on them.

The structure 

When you remove everything from your greenhouse for an annual cleaning, don’t neglect the frame.

Regardless of its construction, wash the structure–NOT the polycarbonate panels–with an oxygen bleach solution. Wood frames are more likely to allow tiny pests to burrow in the cracks and crevices.

Apply a vegetable-based horticultural oil to all exposed wood areas. Using a brush is your best bet to make sure that you cover any areas that unwanted pests could be hiding in. This will also prevent the wood from rotting.

If your greenhouse has a metal frame, the oxygen bleach solution should do the trick.

The plants and soil 

The greenhouse itself isn’t all you have to pay attention to. Regularly removing unwanted vegetative waste can prevent diseases and pathogens from infecting healthy plants.

Compost any diseased or pest-ridden plants in an area outside of the greenhouse.

Since soil contains multitudes of microbes & tiny creatures, it can also contain unwanted diseases and pathogens. During your annual cleanout, replace old soils with clean, disease-free soil.

You can also take preventative measures to avoid contamination such as properly spacing your plants apart. Always practice good hygiene while in your greenhouse and be mindful of what you may be bringing in from other areas. Diseases and pests can be transferred from your clothing and shoes, so be sure to avoid recontamination.

A clean greenhouse is a healthy greenhouse!

Pots and equipment

Wash all of the accessories used in your greenhouse. Wash pots and tools with warm soapy water, then let them sit in an oxygen bleach solution. As a rule of thumb, use 3/4 cup of oxygen bleach to one gallon of water. After a few minutes, simply rinse the equipment and dry it with a clean towel.

If you use disposable seed trays and pots, replace them with new sterilized ones.

Yep, I know it’s tempting to re-use seed trays & pots. But the last thing you want is to transfer disease from an old pot to your tender new plants.

The floor 

Maintain cleanliness in your greenhouse by regularly sweeping the floor.

This way, when your annual cleaning comes around, the process will be much easier. This goes with all aspects of taking care of a greenhouse. The more you attend to it as you go, the easier a complete cleanup will be.

With just a few minutes of ongoing maintenance each day, you can prevent unwanted pests and diseases from ever finding a home in your greenhouse.

That being said, you can make the job go by a lot quicker by using a vacuum to clear out debris.

Irrigation and holding tanks

To clean irrigation lines and holding tanks, use the oxygen bleach solution. Scrub any holding tanks with the solution and flush the lines out.

The irrigation system can develop algae and be a spawning ground for unwanted bacteria & fungi–especially if you irrigate your plants from a nearby pond. So, make sure to disinfect all parts of your irrigation system to prevent contaminating your plants & soil.

Seriously, you don’t want to water your plants with disease-ridden water.

Preventative measures

In addition to regularly cleaning your greenhouse, there are preventative measures that you can take to lessen the chances of those annoying pests coming in.

Most common pests are drawn to humid environments, so maintaining a consistent temperature and humidity is important.

That being said, investing in a quality ventilation system is one of the single most helpful things you can do for your greenhouse.

Without fresh air circulating through your greenhouse, plants are much more susceptible to fall victim to opportunistic bugs. Even simply placing a fan near affected plants can cause pests to pack up and leave your greenhouse.

The biggest thing you can do though is tidy as you go. When you take care of your greenhouse regularly, even if it’s only a couple of minutes each week, it’ll make your end-of-season cleanup that much easier.

Related questions

Can you use Windex on polycarbonate?

Windex is NOT safe to use on polycarbonate, since, like with any solvent, it can damage the polycarbonate. Dishsoap or a polycarbonate-specific cleaning product is best, and will prevent damage.

Can you clean polycarbonate with alcohol?

Polycarbonate can be damaged if you use solvents, even alcohol–whether isopropyl or rubbing alcohol. So, mild soap & water is best. And make sure to use a soft sponge–polycarbonate can scratch very easily.

How do you clean a polycarbonate roof?

To clean a polycarbonate roof, follow the same instructions as above: use only dishsoap, and a wet non-abrasive sponge. Polycarbonate scratches very easy, so hose down the roof before gently wiping it down with non-abrasive cloth. Use a ladder or scaffolding to reach high & hard-to-reach areas.

Greg Volente

Greg Volente holds a Naturalist Certificate from the Morton Arboretum, worked for The Nature Conservancy leading environmental education programs and doing natural areas restoration, and worked in the soil science research & testing lab at Michigan State University. Besides gardening, he's an avid wildflower enthusiast, and loves botanizing, hiking, and backpacking.