Microbiological hazards can occur when foodstuffs come into contact with contaminated surfaces or infectious agents dispersed by air currents in the manufacturing environment. An environmental monitoring program (EMP) is a critical aspect of sustainable and safe food manufacturing used to evaluate the effectiveness of the microbial controls in place. An effective EMP should be based on risk analysis, taking into account previous sampling history to determine the selection of the sampling points, the scope of the test, and the frequency of analysis. This study involved evaluation of the environmental monitoring regime and microbiological status of a medium-sized dairy plant manufacturing food ingredients, e.g., proteins, milk powders, and dairy fats. The data specific to microbial tests (n = 3,468), recorded across 124 fixed sampling locations over a 2-year period (2014 to 2015) from air (n = 1,787) and surfaces (n = 1,681) were analyzed. The aim of this study was to highlight the strengths and weaknesses of the EMP in a select dairy processing plant. The results of this study outline the selection of sampling locations, the scope of the test, and the frequency of analysis. An analysis of variance revealed subsections of the manufacturing areas with high risk factors, especially the packaging subsection specified for bulk packaging, the atomizer, and the fluidized bed. The temporal and spatial analysis showed the potential to reduce or relocate the monitoring effort, most notably related to total coliforms and Staphylococcus aureus, across the dairy plant due to homogeneity across the sampling subsections with little or no deviations. The results suggest a need to reevaluate the current EMP and the corrective action plan, especially with regard to detection of pathogens. Recommendations for optimization of the EMP are presented to assist the dairy industry with reviewing and revising the control measures and hazard assessment with regard to existing contamination issues.