Antimicrobial prophylaxis aims at decreasing the risk of surgical site infections (SSI) by administration of antimicrobial drugs prior to surgery in animals at risk. Multiple risk factors for the development of SSIs have been determined in companion animals, and based on these risk factors, a flow diagram is proposed to identify dogs and cats that would benefit from antimicrobial prophylaxis. Furthermore, the most identified bacteria in healthy companion animals are listed per organ system with their recommended prophylactic antimicrobial drug(s). Besides administration of the optimal drug type, the route of administration, dose, dose interval, and duration of antimicrobial prophylaxis are important to help reduce the emergence of (multidrug-) resistant bacteria.