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Crop clean out: Tips and tricks

A thorough clean out can reduce carryover of pests and pathogens. Have you covered every nook and cranny?

September 15, 2020  By Cara McCreary

Start with a clean greenhouse before planting to help set up your IPM program for success. Image credit: OMAFRA

As many greenhouse vegetable crops start to wind down, it is critical to conduct a thorough clean out between crops. Not only can this reduce carryover of arthropod pests and plant pathogens, it also improves the success of integrated pest management (IPM) programs in the next crop.

Here are three critical steps to a thorough cleaning:

1. Remove organic matter (OM): Why?
Because OM protects pests and can neutralize/inactivate disinfectants.


2. Wash with detergent, rinse, dry: Why?
Because washing/scrubbing with detergent first can eliminate more OM and begin to break down pathogens.

3. Disinfect, rinse, dry: Why?
Because this final step can catch what was missed in steps 1 and 2.

Tips to keep in mind during clean out:

  • Maintain warm temperatures to starve pests and increase efficacy of disinfectants
  • Monitor for residual pests
  • Maintain sanitation and hygiene (e.g. footbaths, hand sanitizers, freshly laundered clothes, clean footwear, etc.)
  • Heat and vent to rid greenhouse of pesticide residues after clean out to avoid phytotoxicity in your next crop

Clean out Checklist

Keep this checklist handy to make sure you’ve covered all your clean out tasks.

Crop disposal

♦ Treat crop before removal to kill active pests

♦ Remove and properly dispose of:

  • Old crop – do not pile or spread infected plant material behind your greenhouse
  • Other materials (clips, slabs, strings, etc.)

♦  Remove remaining plant residues; sweep and vacuum focusing on gaps in floor covering, walkways, corners, ledges, etc.

Clean irrigation system

♦ Remove drippers from media; keep lines slightly charged to maintain moisture

♦ Disconnect pH and EC sensors

♦ Remove filters

♦ Flush lines:

  1. Flush with water
  2. Flush with acid (e.g. nitric acid, sulfuric acid, hydrochloric/muriatic acid); check the emitter manufacturer for pH requirements
  3. Pulse several times at 1-hour intervals for 24 hours
  4. Flush with clean water
  5. Flush with disinfectant
  6. Flush again with clean water when specified by the product label

♦ Clean and disinfect:

  • Stock tanks, return/dirty leach tanks, freshwater tanks
  • Pump sets
  • Emitters stakes (soak in acid solution for up to 48 hours, rinse well, disinfect, rinse well when specified by the product label)

♦ Replace emitters and other parts when necessary

Washing and disinfection

When washing and disinfecting different parts of the greenhouse, be sure to let soak (wet) for a minimum of 15 minutes up to 60 minutes. Though longer contact time is generally more effective, be mindful of corrosiveness of disinfectants. Rinse well with water and let dry completely between steps. Do not forget door handles, keyboards and other surfaces touched by employees.

♦ Wash and disinfect structure

  • Use a power washer or some specialized equipment on low pressure with large opening tip
  • Start at the point of the roof and work down
  • Replace old floor covering when necessary

♦ Wash and disinfect all horizontal surfaces, including:

  • Rafters
  • Pipes
  • Troughs
  • Concrete walkways

♦ Wash and disinfect all tools and equipment, including:

  • Scissor carts
  • Picking crates
  • Wires
  • Machinery
  • Vehicles
  • Fork lifts (including forks)
  • Pallets
  • Knives and scissors

♦ Wash and disinfect other common areas, including:

  • Offices
  • Washrooms
  • Lunch rooms
  • Packing lines
  • Boiler room

Gone through the checklist above? Now you are ready for planting!

Disclaimer: Always check federal, provincial and municipal regulations when choosing pesticides and disinfectants. It is critical to store, handle, apply and dispose in a proper manner to avoid or eliminate negative impacts on personal health and safety and the environment. Always check safety data sheets (SDS) recommendations before using any product. Check warning labels for required personal protective equipment (PPE).

Cara McCreary, MSc., is the greenhouse vegetable IPM specialist with the Ontario Ministry of Agriculture, Food and Rural Affairs. She can be reached at .

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