Recent scientific investigations underscore the pivotal role of food-associated desired microorganisms in promoting human health and wellness. The Mediterranean diet (MD), recognised for its comprehensive health benefits and nutrient-rich profile, has also become a key focus in this field. By synthesising findings from both literature and laboratory-based culture-dependent analyses, we categorised MD food items according to their microbial characteristics. We have also developed some case studies simulating home preparation to assess the impact of vinaigrette (olive oil, vinegar, and salt) addition on the microbial content of salad and the effect of pasta preparation with pecorino cheese on microbial load (i.e., pecorino added grated to warm pasta; pecorino added to cold cooked pasta; prepared pasta with melted pecorino; sautéed pasta). Additionally, we highlighted the negative effect of pasteurisation on dietary microbes associated with fermented foods, using fermented table olives as a model product. These analyses supported the design of low- and high-microbe intake diets.