Microbial communities are likely to undergo consistent development on food matrixes that represent significant nutritional supports for their growth. Processes, additives and preservatives do represent striking drivers for shaping them. These communities weave complex interactions that lead to the production of metabolites that can alter food products and limit their preservation. The ability to identify the actors of these ecosystems, their activities and their interactions is at the heart of the ability to control food preservation. Finally, the next goal is the ability to predict these interactions in order to decipher about the status of the foods and their safety. From the challenge of identification to the challenge of understanding, comprehensive analyses have underlined the role of different species and their balance in the ecosystem, their functional structure, their trophic flexibility and finally their competiveness, leading either to spoilage or preservation. These explorations pave the way for the future development of microbial solutions through ecological engineering.