Fermentation has been an integral process applied to products constituting the human diet since ancient times and fermentation processes passed from sacred ceremonies of community sharing to everyday life meals, regardless of the cultural society concerned (Garine et al.,2001). However, fermented foods remain a partial mystery that tools such as proteomics can investigate deeper. Proteomics has recently helped archeologists to decipher the ancient human dairy activities from at least the 2nd century BC and to show that they were close to those used at the present time namely for Kefir making (Hong et al., 2012; Yang et al., 2014). Fermented food products represent up to 30% of our daily diet and are the major source of ingested living bacteria (Olivares et al., 2006). Dietary deprivation of fermented food products causes a decline in the innate immune response that can be prevented by the consumption of yogurt (Olivares et al., 2006), highlighting the important role of fermented milk products in the human diet. This is supported by the fact that yogurt is one of the very few alleged fermented products with an EFSA-accepted functional claim, regarding lactose intolerance alleviation (EFSA Panel on Dietetic Products, 2010). Milk fermentation was a prerequisite for its conservation in the absence of the cold chain. Hundreds of fermented milk products have evolved throughout the world and these products possess varied appearance, texture, flavor, taste, and health benefits, thanks to the association of various microorganisms with milk (and its derived product the whey) and with human knowledge. Fermented milk products, that is, yogurts, fermented milks used as beverages such as Kefir and Koumiss, and a huge number of cheeses, harbor ecosystems ranging from simple to highly complex. They consist of (1) milk matrices arising from various mammals (cow, goat, ewe, mare, camel, yak, etc.) having a variable composition in proteins, lipids, carbohydrates, minerals and (2) microorganisms belonging to various phylogenetic groups (firmicutes, eukaryotes, proteobacteria, and actinobacteria) present within and at the surface of the product, most notably on some cheese varieties. Proteomic investigations are particularly relevant for such food products, as proteins act both as the supplier and substrate of enzymes, during milk proteolysis and degradation of bacterial proteins, a point that is addressed by peptidomics. Furthermore, bacteria in these products also have dual functionality as producers of bioactive compounds and as probiotic agents. The increase in the number of sequenced genomes facilitates greater knowledge of the bacterial machinery. Only proteomic tools are able to show definitively the end products of the enzymatic machinery and thus assess its efficiency within the milk environment and through the technological processes applied. However, hedonic quality and health properties cannot be extrapolated to all fermented milk products. The remarkable biodiversity in substrates and microorganisms requires fine characterization of each fermentation process and/or functional fermented foods. In this chapter, we will give an overview of the major breakthroughs performed thanks to proteomics analyses: from pure culture to complex fermented products such as cheeses, with a particular interest in fermented milk product quality and probiotic effects.