The growing demand for more sustainable food systems has driven the development of solutions based on food microbiology, capable of integrating safety, functionality, and environmental responsibility. This paper presents a critical and up-to-date review of the most relevant advances at the interface between microbiology, sustainability, and food innovation. The analysis is structured around three main axes: (i) microbial fermentation, with a focus on traditional practices and precision technologies aimed at valorizing agro-industrial waste and producing functional foods; (ii) microbial biocontrol, including the use of bacteriocins, protective cultures, bacteriophages, and CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated)-based tools as alternatives to synthetic preservatives; and (iii) the development of functional foods containing probiotics, prebiotics, synbiotics, and postbiotics, with the potential to modulate the gut microbiota and promote metabolic, immune, and cognitive health. In addition to reviewing the microbiological and technological mechanisms involved, the paper discusses international regulatory milestones, scalability challenges, and market trends related to consumer acceptance and clean labeling. Finally, emerging trends and research gaps are addressed, including the use of omics technologies, artificial intelligence, and unexplored microbial resources. Food microbiology, by incorporating sustainable practices and advanced technologies, is positioned as a strategic pillar for building a healthy, circular, science-based food model.