Maintaining a clean coop is important to reduce the potential for disease transmission. To maintain good sanitation, you will need to periodically clean your coop. Good sanitation includes proper cleaning and disinfection of your coop. Big picture, proper cleaning and disinfecting (and we’ll go over the difference between the two) are crucial in order to prevent exposure to multiple infectious diseases including Marek’s disease, Salmonella and ectoparasites like mites.

As an example, let’s say your neighbor gave you their coop and you wanted to clean it before you start your flock or simply that you want to clean out your coop because it’s been a while and it’s pretty disgusting … So now let’s go over the basics of how you might approach this

  1.     Start by removing all birds and equipment like feeders and waterers from the coop to be cleaned.
  2.     Dry Cleaning: Sweep all the loose dirt off ceilings and walls. Scrape and remove all the remaining poop and dirt from perches and roosts. Remove as much dry material as possible. Remove all feed from feeders.
  3.     Wet Cleaning: Wet cleaning is done in three steps: soaking, washing and rinsing. Make sure you use warm or hot water
  4.     Soaking: Soak the heavily soiled areas (perches and roosting areas, floors, etc.) thoroughly. Use a low pressure sprayer to totally soak all surfaces. Soak until the accumulated dirt and manure has softened to the point it is easily removed.
  5.     Washing: Wash every surface in the coop where dirt and dust may accumulate. You have a lot of different choices but I like to use good old fashioned dish soap mixed with hot water (160°F or hotter is best). Manual scrubbing with a moderately stiff brush is one of the best ways to insure a thorough cleaning. Make sure you inspect all the surfaces to confirm all the dirt and manure has been removed. 
  6.     Rinsing: A final rinse immediately after washing helps remove any residues. Make sure you mop up puddles as they can rapidly become breeding grounds for bacteria.
  7.     Disinfecting: This is a crucial step. Disinfectants should be applied only after the building and equipment have been thoroughly cleaned, ideally right after rinsing. Disinfectants can be applied by sprays, aerosols or fumigation. The types of disinfectants generally used are phenolic compounds (e.g., Pine-sol, One Stroke, Osyl),  iodine or iodophors, (e.g., Betadine and Weladol), chlorine compounds (e.g., Clorox, generic bleach), quaternary ammonium compound (e.g., Roccal D Plus) and oxidizing compounds (e.g., Virkon S). They all have advantages and disadvantages which are beyond the scope of this article, but whichever one you choose make sure they are applied on surfaces without organic material (aka poop, dirt) since those materials will inactivate the disinfectant. For a more thorough disinfecting, soak waterers and feeders in a 200 ppm chlorine solution (1 tablespoon chlorine bleach per gallon of water). 
  8.     Drying: Thoroughly air-dry the coop. Open any windows/doors to facilitate ventilation. Ideally pick a dry sunny day to make this go faster. 

It is really important to realize that environmental factors all connect together. For example, if it is really hot and humid or if the waterers are not clean your chickens will most likely eat less feed, and this problem is compounded if both happen at the same time. If they are eating a bunch of chicken scratch already they will not get their 4 grams of Calcium to support egg production.