Good Greenhouse Hygiene

By Chris Bond
Published: October 23, 2018 | Last updated: April 23, 2021 02:59:23
Key Takeaways

Plants are more likely to thrive in a clean environment. Make it your goal this spring to carry out these simple sanitary measures in your greenhouse, and start the growing season out right.

One of the most effective ways to protect greenhouse and indoor-grown crops and plants from attracting insects or contracting diseases is observing proper sanitation practices. Keeping up this regimen on a regular basis is cheap insurance to ensure the health of your crops. The following considerations will help you keep up an ideal growing environment for your plants.



Maintaining a weed-free environment is one of the most basic steps you can take to keep your greenhouse clean. In addition to competing with your plants for nutrients, water, sunlight, and space, weeds in your growing area can be a food source and a haven for pest insects. Make sure to pull them out as they appear. This includes weeds in pots and trays as well as those that germinate and root themselves in the floor.

Check any drainage areas for weeds as well. The nutrient-rich sludge that collects in drainage areas is a nurturing environment for many weed species. Watch for weeds on the outside of your greenhouse and in the gutters, as seeds can easily enter growing spaces via the ventilation system, wall cracks and the simple action of opening and closing doors.


Using herbicides to control weeds is not advisable as you can inadvertently cause more damage to your crops than the presence of weeds could cause. Pull weeds by hand, or cut them out if they are deeply rooted. Cutting needs to be done repeatedly to be effective, as weeds will grow back from the energy is stored in their root systems until you can exhaust the supply.

Smothering weeds with a dark cloth or tarp is another effective way to deal with them. Make sure to leave them covered long enough to prevent weeds from photosynthesizing. If weeds around the periphery of your greenhouse or growing area are too numerous to eradicate, control them by cutting their flowers so they do not set seed.

Floors, Walls & Ceilings

Cleaning your greenhouse or growing area from top to bottom is a good idea. This is not always practical when you are actively growing, but should be done whenever possible. Always start from the top down. If the ceilings are low enough, use a broom to knock down any spider webs or debris. If ceilings are too high to reach, use a pressure washer to rinse off the ceiling and walls of the greenhouse.


This should dislodge debris and hopefully any pest insects hiding in the cracks and crevices. If you’re using a gas-powered pressure washer, make sure the engine is outside the building to avoid breathing in carbon monoxide.

Sweep or use a leaf blower to rid the greenhouse of all debris and dirt on the floor. As with the pressure washer, do not use a gas-powered blower inside. An electric blower is a good investment to aid in greenhouse sanitation. Floors should be cleaned in a greenhouse or grow room weekly, if not daily. This is the most likely area—other than the plants themselves—for insects and diseases to be lurking.


After the ceiling, walls and floor have been swept, blown out and rinsed, apply a disinfectant, such as bleach, quaternary ammonium or a peroxide solution, to all of those surfaces. A power sprayer, pressure washer, backpack or even a handheld pump sprayer can be used. If you do not have access to any of these, a syphon assembly can be inexpensively obtained and connected to the end of your hose.

The syphon’s tube can be placed into a bucket of cleaning solution, which will be mixed with the water from the hose as it comes out. A fertilizer injector can be used for this purpose as long as it is thoroughly cleaned before and after use to avoid a toxic dose of disinfectant being delivered to plants.


During a major cleaning of your greenhouse space, fixtures such as fans, louvers, and vents should be cleaned using the same method as described above. The fixtures should also be wiped down periodically between major cleanings to reduce the incidence of airborne mites and pathogens. Consider doing this monthly, if not weekly. In addition, grow lights and ballasts should not be overlooked. Take all of the usual precautions before cleaning—unplug them and make sure they are completely dry before plugging back in. If this is not feasible, they should be dusted, wiped off and covered in plastic while the rest of the room is being cleaned.

Tables & Work Areas

Like fixtures, tables and work areas in the greenhouse should be cleaned and sanitized regularly. When there are plants on them and a complete clean is not possible, just make sure there is no debris or soil on them. If you leave potting soil exposed in an area devoted to transplanting, make sure to keep it covered when not in use. A leaf blower can be used to blow debris off of tables and work areas even when there are pots on them, so long as your blower has multiple settings. If it does not, sweep and wipe the tablespace as often as is needed.

Between crops, all tables and work areas should be sanitized using a disinfectant as when cleaning the entire space. The amount of solution used will vary depending on which products you’re using and whether you are undertaking a maintenance cleaning or a thorough cleaning. As always, consult the label of whichever product you use.

Hoses & Watering

The first time water is turned on for the day, or after long periods of inactivity, the initial discharge of water should be directed into the drain. This should be done for 30-60 seconds to expel sediment in the line or any insects or pathogens that have set up camp in your hose. For this reason, prevent the end of the house from making contact with the floor.

As the water is running, manually check the water temperature. During warmer months, the lines that carry water heat up quickly and can raise the water temperature to near boiling. Discharging this hot water onto plants can weaken their root system, making them more susceptible to insect and disease infestation. In many cases, applying boiling hot water can kill plants, too. The same is true during colder months. Near-freezing water temperatures can shock the root systems of plants that have not been acclimated to the cold, resulting in stressed plants that are more susceptible to pathogens and predators.

When watering plants, it is a good rule of thumb—though not always possible—to avoid getting water on the foliage, especially on cloudy days. This excess moisture doesn’t always evaporate and can provide a good environment for fungi to grow. Determine if the plants can go without water during cloudy and overcast days. It is better to let plants get slightly dry in between waterings than to create disease-favorable conditions. When irrigation is needed, it should be performed in the morning or early afternoon.


It is not uncommon to collect spent blossoms, dead plants, stems and used soil in a bucket to be added later to a compost pile. While this is an admirable practice, containers need to be emptied on a daily basis. When left in the greenhouse for a prolonged period of time, these materials start to decompose quickly in such containers, especially when closed, and release ethylene gas.

While ethylene gas is a natural and necessary part of the ripening process, too much is detrimental to your crops. Premature blossoming, unwanted growth, fruit ripening, leaf and fruit senescence, and leaf and fruit abscission are among the many effects of overexposure to ethylene gas. These containers of undesirable biomass are also an inviting area for insects and diseases to fester. Periodic disinfecting of the containers should be done with a bleach solution or similar product.

Pots, Containers & Tools

Used pots should be disinfected before use with a bleach solution or equivalent. All organic matter should be removed prior to disinfecting. Hand tools such as pruners and trowels and anything that will be making contact from plant to plant should be disinfected with hydrogen peroxide, isopropyl alcohol or an equivalent. For certified-organic growers, or those who follow organic practices, there are several disinfectants on the market compatible with organic food production.

A Final Note

Recall the disease triangle, which consists of a causal agent like a pathogen or pest, a hospitable environment—think too much moisture, humidity or temperature—and a susceptible host. If you can prevent any one of these conditions in your greenhouse environment, you will be laying an excellent foundation for your garden’s survival and success.


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Written by Chris Bond | Certified Permaculture Designer, Nursery Technician, Nursery Professional

Profile Picture of Chris Bond

Chris Bond’s research interests are with sustainable agriculture, biological pest control, and alternative growing methods. He is a certified permaculture designer and certified nursery technician in Ohio and a certified nursery professional in New York, where he got his start in growing.

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