Microbial spoilage is challenge for a range of food industries and is also a major contributor to global food waste. In order to prevent and reduce microbial food spoilage, evidence-based strategies must be implemented throughout supply chains. To this end, the studies presented here contribute to (i) methods for monitoring spoilage microorganisms, (ii) improved understanding of sources and mechanisms of transmission of microorganisms into food, and (iii) potential strategies to implement at the various points in food supply chains aimed at preventing and reducing microbial spoilage. While microbial spoilage originating from sources throughout the food chain is an issue for many sectors, the studies presented here focus specifically on dairy and fresh produce. In the area of dairy quality, we provided insights into spore enumeration methods for milk powders and identified a set of methods that captures a wide range of variation in spore count across powders. We also contributed to understanding of routes of transmission of spoilage microorganisms into raw milk; specifically, we found bedding material had a direct influence on levels of spores in unused and used bedding, as well as an indirect association with spore levels in bulk tank raw milk through used bedding spore levels. Furthermore, we identified strategies at farm and processing levels for reducing microbial spoilage of dairy products. At the farm-level, we identified specific bedding and farm management practices associated with spores in bedding and bulk tank raw milk. At the processing-level, we identified important quality management practices associated with fluid milk spoilage due to post-pasteurization contamination, including cleaning and sanitation, employee training, and quality testing programs. Preventing microbial spoilage is also challenge for the fresh produce industry, yet relative to dairy, research in the area of microbial spoilage of fresh produce has been limited. Our foundational study of bacterial dynamics on spinach for a supply chain located in Northeast China, from point-of-harvest through shelf life, improved understanding of factors associated with spinach spoilage. Overall, these studies expand our understanding of microbial spoilage of dairy foods and fresh produce and will facilitate implementation evidence-based strategies for preventing and reducing microbial spoilage.