Confectionary products are often considered relatively inert from a microbiological perspective. Nevertheless, several Salmonella outbreaks have been attributed to confectionary, particularly chocolate products. The cause of these outbreaks was generally traced back to lapses in GMP, particularly cross contact issues and water ingress. Managing Salmonella in chocolate manufacture begins with a validated cocoa bean-roasting process. However, the potential for pathogen recontamination exists with the addition of ingredients and inclusions post process. This risk can be managed by a stringent supplier assurance program including prerelease microbiological testing of these materials. In addition to assured ingredients, the manufacturing environment must include a strict containment policy for raw and finished goods, control of water use including the prevention of water leaks, and ongoing microbial surveillance. Manufacturing equipment needs to be hygienically designed and amenable to sanitation processes, should a contamination event occur. Lastly, an effective microbiological verification program is essential to ensure all described processes are in control.