A routine cleaning will help prevent unwanted pests and disease.

Editor’s Note: This article has been updated.

Greenhouses extend the growing season for tomatoes and peppers and offer the opportunity for citrus in northern climates. For most gardeners, greenhouses are a dream addition to the garden, a safe place for tender plants. But greenhouses also need maintenance.

Why clean your greenhouse?

Whether made from glass, polycarbonate or polyethylene plastic, greenhouses benefit from periodic cleaning and maintenance. A routine or annual cleaning is essential to prevent unwanted pests and diseases from moving in. While this protected environment nurtures plants, it also provides the perfect conditions for pests to thrive or overwinter. Insects and mites will hibernate in cracks and crevices, plant pathogens will continue to exist in the soil, algae will grow in the lines, and gnats will reproduce on organic residues.

While maintenance should take place regularly for year-round greenhouses, a fall clean up at the season’s end is enough for the seasonal greenhouse.

These are risks to any plants you are hoping to foster come springtime, and success requires a combination of removing crops, disinfecting, preparing, and sanitizing. While this maintenance should take place regularly for year-round greenhouses, a fall clean up at your season’s end is enough for the seasonal greenhouse.

Stop overwintering pests and diseases

Some pests and diseases are more likely to overwinter in a greenhouse. Thankfully you can usually predict what they’ll be by paying attention to the type of crops you are growing.

The following list details pests and diseases most commonly associated with greenhouse environments. If you have experienced any of these in the past, a greenhouse clean up is even more essential for prevention.

Affected crops
Damping offSeedlings display brown lesions at the base close to the soil line. Once affected, plants will topple and die.Seedlings of most crops.
Tomato blight (early and late)Brown spots occur on leaves located at the base for early blight or on stem tips and leaves for late blight.Tomatoes and potatoes.
Powdery mildewStarts as small, white, powdery spots affecting the lower leaves and stems of plants. As disease progresses, white powder will cover the entire plant.Vegetables, ornamentals, annuals, shrubs.
Gray mold (Botrytis)Affects tender parts of the plant. Leaves will discolor, stems will wilt, buds will fail to open, and masses of gray spores may develop.Vegetables, fruits, starts.
WhiteflyUsually first discovered by sticky, honey-like substance on the tops of the leaves that will later develop a black sooty mold. The juveniles are observed as very small, green scales on the underside of new leaves. The adults, which are small but more noticeable, are very tiny, white and moth-like in shape, showing up in clusters around new shoots and leaves.Most tender greenhouse or tropical plants.
Spider miteNew leaves will show yellow stippling, with small webs between shoots. Over time, leaves will completely yellow and webbing will be thick. Most tender greenhouse plants and many tender greenhouse tropicals.
Fungus gnatsFungus gnats love rich organic matter high in moisture. The gnat larvae feed on plant roots causing stunting, wilt, and yellowing of leaves. The adults are often seen flying close to the soil surface depositing eggs.A multitude of hosts. Anywhere moist soil is available.

Cleaning your greenhouse step-by-step


  • Choose a time when the weather is favorable for a few days and empty the greenhouse of all plant matter, including any weeds that are trying to get a foothold on earthen floors.
  • Take note of any existing diseases or pests and dispose into a compost away from susceptible plants.
  • Inspect any citrus or tropical plants for developing colonies of scale, mealy bug, whitefly, or spider mite. Use safe management techniques and quarantine until the problem fully resolves. For more information, read our article about Spider Mites: How to Identify and Control Them Naturally.

Pots and accessories

  • Wash all greenhouse accessories—including pots, trays, and equipment—thoroughly with soapy water and let sit in a oxygen bleach solution of 3/4 cup oxygen bleach to one gallon of water.
  • Recycle or dispose of disposable seed trays and pots, moving them far from the vicinity of the greenhouse as soon as possible.


  • Old soils can contain pathogens like pythium, fusarium, rhizoctonia, fungus gnats, grubs, root aphids, and more. Remove soils from pots and beds and let compost for a year or more to rejuvenate.
  • Replace with clean, disease-free soil purchased at a reputable supplier in the spring or just prior to planting new crop. This includes the soil in your pots and beds as well as the soil between paths and under benches.
  • Rake or sweep out any debris and treat the entire exposed area with diatomaceous earth at the very end of the clean up procedure when your greenhouse will sit dormant.


  • Disinfect irrigation and holding tanks. Irrigation lines and holding tanks develop algae and can host thousands of gnats, which are a threat to small roots. Using 3/4 cup oxygen bleach to one gallon of hot water, flush lines, soak any dripper heads, and scrub out holding tanks or fertilizer reservoir.

Structure and wood

The greenhouse structure provides great refuge for overwintering pests. Metal frame greenhouses aren’t as susceptible but still need disinfectant. Wood is the worst for providing the right cracks and crevices that spider mites, thrips, aphids, and whitefly all use as a hideout.

  • Wash your entire greenhouse structure and glass down using an oxygen bleach solution.
  • Apply a vegetable-based horticultural oil onto all exposed wood. This is best done using a brush to ensure the oil reaches into any cracks to suffocate hiding pests.
  • Let the greenhouse sit empty and dormant over the winter or for as long as possible. Ensure clean soil is used to replace previous soils and only introduce pest and disease free plants.

Ongoing greenhouse cleaning and maintenance

Throughout the growing season, avoid overlapping planting or intercropping to reduce transferring problems from one crop to another.

  • Deal with “green bridges” or weeds and volunteer plants that can act as hosts for problems between crops as quickly as possible.
  • Remove plants that develop diseases or harbour pests from the growing area as soon as they are noticed. This will not only limit the spread, but also make clean up easier.
  • Avoid recontamination. Disease and pests can be transferred from one place to the next on shoes, clothing, and new plants.
  • Practise good hygiene and do not visit the greenhouse after visiting areas of potential threat.
  • Always wash pots to be reused and disinfect your tools on a regular basis. The more effort you put in the less risk you will have.

A clean slate

Taking the time for greenhouse cleaning and maintenance at the season’s end will save you time and energy come springtime. You can also rest easy knowing that any crops entering the greenhouse next year will have a better chance to survive and thrive.

View Eartheasy’s full line-up of greenhouses and accessories.

Responses (0)