Thorough cleaning is necessary to prevent cross-contact when processing different products, and it is useful to validate that cleaning has been done to remove any allergen. Workers can visually inspect equipment to ensure there is no residue, film, or sheen. Chemical tests can be used to test for residues, including peanut-specific Adenosine triphosphate (ATP) test kits.

Equipment, tools, and surfaces must be thoroughly cleaned before processing product that does not contain the same allergens. Alternatively, a factory may dedicate tools, equipment, or entire lines to specific processes, which reduces the need to clean for allergens. Color coded labels on equipment can be useful.

Training employees how to clean and use separate tools for allergen prevention is very important.