Greenhouse Cleaning and Disinfecting: 5 Essential Steps to Kickstart Your Season

Why spend your efforts on cleaning and sanitizing? 

Greenhouses provide ideal conditions for pests and pathogens, making sanitation critical. A successful crop season starts with a clean slate. Investing time and money in maintaining a greenhouse's cleanliness greatly outweighs the costs associated with frequent pesticide use and crop losses due to unsanitary conditions. Just like how regular dental care keeps cavities at bay and saves you from bigger dental woes down the line, greenhouse sanitation is a proactive measure. While the immediate benefits might not be obvious, this approach ultimately safeguards the health of your plants and, importantly, your wallet. 

Treat your crop BEFORE removal: 

Before you knock down your crop, it is crucial to tackle pests that hide and overwinter in the nooks and crannies of your greenhouse. Treating your plants right after the final harvest is a proactive step to prevent these pests from migrating outdoors or lingering to affect your next crop cycle. There are two effective treatment methods: chemical and heat. 

Chemical Treatment: This involves using a horticultural oil or soap to thoroughly coat your plants, as well as the troughs and ground surfaces. A smart approach is to start spraying from the back of the greenhouse and move towards the front. This method ensures that you don’t have to walk through already treated areas, which could compromise the treatment’s effectiveness and your own safety. 

Heat Treatment: As the term suggests, this method requires heating your greenhouse to a level high enough to eliminate all active pests. The recommended temperature is around 40°C (104°F), sustained for at least four days. This technique is particularly suitable for crop cycles that end in the summer months when maintaining such high temperatures is more economically feasible. 

Keep plant material FAR away from the greenhouse.  

Some growers put plant waste material behind their greenhouse. Of course, the waste will decompose over time, but these growers sometimes forget that all sorts of contamination and diseases can be hidden in this waste. 

To minimize the survival and dispersal of pests and diseased tissue, remove and properly dispose of residual crop debris immediately. Surface burying plant residues into the soil in adjacent fields is not sufficient. For example, bacteria responsible for bacterial canker can survive on surface residues for at least 24 months. In contrast, deeply burying the same debris can significantly reduce their survival to about 7 months. If immediate removal or deep burial of the debris is not feasible, placing it in covered bins and disposing of it at a landfill site is a recommended alternative. 


For the safest route new growing media should be used for every crop cycle. However, that is not always realistic for some farm operations. If you must reuse growing media, always sanitize it by fumigation or steam before starting the next crop cycle. Soil can be a breeding ground for overwintering pests and pathogens that attack roots. 

Thoroughly clean the greenhouse before disinfecting.  

  • Remove Obstacles to Disinfection: Debris can compromise the effectiveness of disinfectants. A clean surface is crucial for effective disinfection. 
  • Systematic Cleaning Approach: Start cleaning from the top of the greenhouse and work your way down, moving systematically from front to back. This ensures that every part of the structure is attended to without missing spots. 
  • Equipment and Machinery: Don’t overlook cultivation equipment and machinery – they are integral to your greenhouse and can harbor pests and pathogens. 
  • Power Washing: After debris removal, power wash the entire structure. Consider using detergents for tougher grime and pay special attention to hard-to-reach areas, especially overhead piping where pests and dirt can accumulate. 

Don’t forget about the irrigation systems 

Healthy crop growth hinges on the proactive maintenance of your irrigation system. Ignoring it could lead to a continuous struggle against harmful pathogens like Pythium and Fusarium. Biofilm is another issue that can develop if proper irrigation system hygiene is not practiced. It is formed from fertilizer sediments and can clog pipes and disrupt water flow. 

To tackle this, consider running acid and hydrogen peroxide through the irrigation system. Always check the pH tolerance with your drip line manufacturer first. After confirming compatibility, thoroughly flush and rinse the lines. Be wary of using chlorine; despite its immediate effectiveness, its corrosive nature can harm your system in the long run. Chlorine can clean water storage tanks very effectively. 

Don't forget about your drip stakes – a simple spray isn't enough. Replace them or soak in a disinfectant for effective sanitation. A proactive approach to irrigation system hygiene is key to ensuring less plant disease issues in the future.  

The “Better safe than sorry” spray.  

Once the greenhouse is emptied and disinfected, it’s advisable to implement a second application of horticultural oil. This step is crucial as many common pests, such as thrips, tend to pupate in the soil. During this pupal stage, they develop a thicker wax layer on their bodies, which offers significant protection against various crop protection agents. To effectively tackle these pests, consider raising the greenhouse temperature to 20°C a few days before planting. This increase in temperature encourages pests in overwintering or pupating stages to become active and emerge. Following this, a final spray with horticultural oil can be highly effective in eliminating these remaining pests. 

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Interested in your parasitoid programs. do you have one for DBM? Trichogramma app ?


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