The Preventive Controls for Human Food (PC) Rule, published in 2015, expanded on the Hazard Analysis Critical Control Point (HACCP) approach by including sanitation, allergen, and supply chain preventive controls for food manufacturing. In a Preventive Controls food safety plan, the process controls are required to be scientifically validated, but allergen and sanitation controls are not. However, food manufacturers should determine if the sanitation and allergen controls being applied in their facilities are adequate to control identified hazards. This work was conducted to determine the efficacy of cleaning practices to control bacterial contamination and soy allergen in a large bakery that manufactures cracker and wafer products. Cracker and wafer lines were subjected to the typical wet and dry-cleaning procedures used in the facility. Pre-cleaning and post-cleaning surfaces were sampled and tested using the following methods: ATP bioluminescence, microbiological sponge, Aerobic Plate Count (APC), Enterobacteriaceae Count (EC), and soy allergen qualitative and quantitative testing. Wet-cleaning and dry-cleaning methods were generally found to be effective for reducing microbiological contamination and soy allergen presence. However, certain areas of the processing equipment, such as the groove between the roller shaft and wall and the lid lip, were found to have higher APC post-cleaning than pre-cleaning. This work highlights the importance of sanitation validation studies that are specific to the equipment being utilized.