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Granted, cleaning your greenhouse might not be as exciting as planting your next crop of seedlings, but a clean greenhouse is a productive & healthy place. Plus, you can keep a lid on those friggin’ gnats.


The best way to clean a greenhouse is with hot soapy water and a sponge or squeegee for the windows, and a brush or vacuum for the floors. However, special cleaners can be used for getting rid of mold & algae. Clean windows & glazing is key because dirty windows won’t allow as much sunlight for plants.


Why should you clean a greenhouse?

Cleaning your greenhouse is important in order to avoid pests, mold and diseases.

While growing crops, it’s common for microbes and algae to accumulate. This can also draw gnats and shore flies to your greenhouse, which are extremely unhealthy for your plants.

Without cleaning, diseases such as Pythium root rot can also accumulate.

If you want to keep your plants healthy & productive, cleaning your greenhouse is essential, as plants are unlikely to grow in a healthy manner if pests and diseases are stunting them. Cleaning your greenhouse regularly helps get rid of and prevent diseases and pests.


How often should you clean a greenhouse?

It’s typically best to clean your greenhouse annually.

Yes, if it can be daunting if you have a large greenhouse.

However, an annual cleaning will keep your plants healthy, and will get rid of overwintering pests and diseases. An annual clean will also help maintain & preserve the life of the structure–especially for wooden greenhouses.

That said, windows & glazing should be cleaned more often–maybe even weekly, depending on whether you notice any grime & buildup.

Dirty windows prevent the sun from entering your greenhouse, which will stunt plant growth. It’s important to take the time to thoroughly clean the windows as often as possible in order to give your plants the sunlight they need to grow and flourish.

What are the benefits of cleaning a greenhouse?

An annual cleaning will prevent pests and diseases from accumulating inside of the greenhouse. Getting rid of these pests and diseases are essential in order to keep your plants healthy, as they can sicken, and sometimes kill, your plants.

Cleaning your greenhouse can also help strengthen the structure of the greenhouse–or at least allow you to identify problems early.

Especially if your greenhouse frame is made of wood, a regular clean can prevent the wood from rotting. Likewise, if you clean once a year, you’ll be able to spot problems in the structure so you can fix them before they become catastrophic.

Prevention of diseases and pests

To flog a dead horse: Cleaning your greenhouse regularly helps get rid of & prevent pests and diseases that could otherwise harm or kill your crops.

First, though, it helps to know what to look for to know if you even have a problem with pests or disease. You should know when certain plants are more susceptible to disease, and when the time comes, you should check for signs of the most common diseases, like:

  • powdery mildew
  • botrytis
  • rusts
  • viruses, and
  • root rot.

Maintaining a fairly consistent temperature & humidity can also prevent pests and diseases from gaining a foothold or spreading inside your greenhouse.

Most of these pests are drawn to humid environments, so one of the best preventative measures is a good ventilation system. A ventilation system will provide a nice breeze inside your greenhouse, which will get rid of any pesky hotspots that pests like to live in.

To prevent diseases and pests from accumulating, you can also use biological control agents (biocontrol). Biocontrol agents are great for your greenhouse because they control infestation naturally, and they don’t harm your plants as other pesticides might. However, be careful with this method, as it can take some time for these agents to locate their prey and start being effective. Check out the image below to see some common pests and their effective biocontrol agents.

Beneficial insects

Image courtesy of:

Cleaning the exterior:


How to clean the windows of a greenhouse?

Cleaning greenhouse windows is easy: warm water, a sponge, and some elbow grease will usually get the job done. Be sure to clean all glazing, since you want to maximize sunlight for your plants.

For reaching higher areas, attach a sponge to a broom handle, or any other long stick. Remember, it’s important for every window to be clean–even the ones that are inconvenient to reach!

Be sure to check for broken glass, and replace those panes & panels right away. Cracked or broken glazing can let heat escape and let unwanted insects & critters into your greenhouse.

What materials do I need?

Cleaning the windows is simple, all you’ll need is a sponge, a broomstick (or any other long stick) and warm water. Using Windex or any other window cleaner is also effective, but be careful with cleaning supplies around plants.

How often should I clean the windows of my greenhouse?

The windows of your greenhouse should be cleaned regularly, maybe every couple of weeks. However, be sure to check the windows every day to be sure that they are clean enough for sunlight to reach your plants.

Cleaning the greenhouse interior:


What’s the best way to clean the inside of a greenhouse?

The best way to clean the interior of a greenhouse is to remove everything inside of it.

Move everything out

Yep, everything. Get all that crap out of the greenhouse–it’ll make cleaning way easier.

That includes pots, plants, shelving, hoses, tools, soil, and any other materials you might have inside of the greenhouse. Move everything out.

Then, turn off the electricity, and make sure any heaters or other machines aren’t plugged in.

When removing plants, if it’s cold outdoors, put them in a shed, garage, or another greenhouse, or wrap them in fleece while you clean. That’ll keep them from freezing.

Sweep & get rid of ailing plants

Sweep the floor to remove any fallen leaves and leftover soil. Throw out any garbage.

That includes dead or nearly-dead plants. Yeah, I know you might want to try saving those li’l guys. But face it, you’re better off without them. Move on. Start with a clean slate.

On a similar note: this is the perfect time to tidy up & trim your plant. Remove dead or infected leaves, and throw them in the garbage. Do NOT compost them–you don’t want to contaminate your compost pile and therefore your soil for future plants.

Weed all the plant beds. This ensures your plants won’t get choked out, but will instead get all of the nutrients they need to grow.

Wash & disinfect

Scrub the walls of the greenhouse and any paths on the floor with clean water and disinfectant.

Yeah, I know you’re eco-friendly, but you also want to kill any pests and disease. The last thing you want is to spend all this time cleaning, only to find out you just freed up space for pests & disease to thrive & contaminate your new plants.

Some common disinfectants for greenhouse cleaning include: quaternary ammonium compounds (like Green-Shield, Physan 20, and KleenGrow), hydrogen dioxide (ZeroTol 2.0, Oxidate 2.0), hydrogen peroxide & peroxyacetic acid (Sanidate), hydrogen peroxide, peroxyacetic acid and octanoic acid (X-3), sodium carbonate peroxyhydrate (GreenClean Pro Granular Algaecide), and chlorine bleach.

That sounds like a toxic stew–I know. But a clean greenhouse is a healthy one, and having disease or pests get a foothold is the last thing you want.

Wash all of your greenhouse materials with soapy water. This includes pots, trays, shelves and any other equipment.

You can also wash the structure of your greenhouse with an oxygen bleach solution. This’ll prevent pests from finding places to live inside of your structure.

What materials do I need?

To clean the interior of your greenhouse, gather up:

  • A broom and rake
  • A sponge
  • An oxygen bleach solution
  • A greenhouse disinfectant
  • Anything you might need to weed the plant beds: gloves, a little shovel, etc.

How often should I clean the inside of the greenhouse?

Clean the interior of your greenhouse at least once a year.

It’s best to do it on a warm spring–or even a warm winter–day. That way, you can take any plants outdoors without worrying they’ll freeze.

Also, by getting your greenhouse cleaned in early in the growing season, you’ll feel great about getting your year off to a clean start (pun intended).


What else to clean?


How do I clean my greenhouse materials?

This might sound redundant, but make sure to clean you cleaning materials too. That way, you’re not cross-contaminating your clean greenhouse with tools that might carry diseases or pests.

In other words, dirty tools can contaminate your clean greenhouse. So, clean your tools after cleaning your greenhouse.

Clean your greenhouse tools & materials with a simple sponge and soapy water. Scrub them down and leave them to dry before putting them back in storage.

How do I clean irrigation and holding tanks?

To clean an irrigation or holding tank, use a ¾ cup of oxygen bleach to one gallon of hot water. Flush all of the lines, soak any dripper heads, and scrub the holding tanks or reservoirs with the solution. This’ll prevent the tanks from developing algae and housing thousands of gnats. Friggin’ gnats… (am I right?)

How do I clean a wooden greenhouse structure?

If your greenhouse has a wooden frame/structure, it’s important to thoroughly clean the wood to prevent the it from rotting.

Wash the frame/structure of your greenhouse–regardless if it’s wooden or not–with an oxygen bleach solution. Then, use a paintbrush to apply a vegetable-based horticultural oil to all exposed wood. This will kill hidden pests and prevent the wood from rotting.



What are the best ways to keep my greenhouse clean?

Keeping a greenhouse clean throughout the year can make the task of annual cleaning way easier. A tidier greenhouse requires less yearly cleanup than one that’s been left to get cluttered & messy for the past 12 months.


  • As you garden, remove any weeds immediately. Get rid of dead leaves.
  • Sweep the greenhouse floor daily or weekly, even without removing everything from inside. This will make sweeping much easier when you do.
  • Wipe down windows or glazing weekly or monthly.

How do I maintain my greenhouse throughout the year, when I don’t have time to clean?

When you don’t have time clean thoroughly, you can still quickly sweep the floor or wipe down surfaces whenever you have a spare minute.

Making sure to throw away weeds and dead leaves can also be beneficial to your plants.

This will keep the greenhouse much cleaner, even if it isn’t the ideal situation. Basically, tidy as you go. It’ll make your annual deep-clean much easier & quicker.



How do I get rid of mold?

Getting rid of mold that has accumulated inside of a greenhouse is actually pretty simple. Just pour vinegar into a spray bottle and spray it wherever the mold has grown.

After allowing the vinegar to sit for a few minutes, wipe it away with a clean washcloth. Then, mix one teaspoon of hydrogen peroxide with one cup of water, and wipe it on the mold with a wet cloth.

How do I disinfect a greenhouse?

After removing everything from inside your greenhouse, you can disinfect the greenhouse with a number of solutions. Some of these solutions can get rid of organic residue and dust particles, while others can get rid of algae and gnats.

Again with the friggin’ gnats… (Here in New Mexico, the no-see-ums get really bad during summer).

Alcohol can disinfect microbes that have accumulated inside of the greenhouse. However, alcohol doesn’t last long and will have to be done more often.

Bleach is the most common disinfectant and can also kill microbes. Bleach must be used in a well-ventilated area–you want to kill germs & mold, not poison yourself.

Hydrogen peroxide is also very effective, although it may be a more expensive option. It can kill a large number of microbes, but it can be harmful to your eyes, so wear goggles when using.

In fact, wear goggles anyway, whether you’re using alcohol, bleach, or hydrogen peroxide. Stay safe!

Related Questions:


How do you disinfect plants?

To disinfect plants, first clean & disinfect the pots they live in. After taking the plants out, soak the pot in a solution of one part bleach to nine parts of water for 10 minutes. Afterwards, put the pots in a solution of dish detergent and water. Using this method of pot-cleaning will keep your new plants–or re-potted plants–healthy.

How do you get rid of mold in a greenhouse?

Using a spray bottle, fill it with vinegar, then spritz areas where you suspect mold might be growing. Let the vinegar sit for a few minutes, then wipe it away with a clean towel or cloth. Instead of vinegar, you can also use a solution of one teaspoon of hydrogen peroxide to one cup water, then wipe down the moldy areas with that solution.

How do you get rid of algae in a greenhouse?

If you suspect that algae may be growing in the water lines in your greenhouse, clean the pipes with either chlorine dioxide, copper ionization or water. Check the lines every week or so to make sure the algae doesn’t recur. Re-clean as needed.

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.