Disinfecting horse stalls and other areas horses use, such as trailers, is important for their health. The need is not only true for stalls and trailers and, in fact, is necessary in other animal areas including dogs, cats and other livestock areas as well. Disinfecting also helps prevent human transmission of disease to horses.
The most important factor in disinfecting in all situations is cleaning the area prior to disinfecting. It has been shown that cleaning removes up to 90% of the infectious organisms. Regardless of the claims the manufacturer makes on the bottle of disinfectant, none of them are effective over organic matter and adult horses produce about 50 pounds of organic matter per day including urine and feces. Also included in organic matter is nasal discharges, material from draining abscesses, blood, and any other type of body fluids and excretions. So until this organic matter is removed by thorough cleaning, disinfectants will not be effective. Thorough cleaning requires a detergent and some manual labor to completely remove organic matter and this requires scrubbing the area to be cleaned. High pressure water sprays are not recommended for cleaning infectious areas because the high pressure can aerosolize infectious organisms and spread them to other areas.
In disinfectants, there is no one-step product that is going to be effective regardless of the advertising claims on these products. Products that claim to clean and disinfect at the same time are not going to be effective. As far as a disinfectant, bleach diluted in water is very effective and inexpensive. Regardless of the disinfectant you choose, follow the label on the bottle as more is not always better.