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The distinct microbiological and physicochemical characteristics of sheep milk enable the production of cheeses with unique organoleptic properties. The scenario of sheep cheeses in Brazil is still uncertain, lacking data and regulations. This study aims to characterize the diversity of bacterial groups with potential pathogenic and/or harmful properties to milk technology and correlate the presence of these bacteria with the physicochemical properties of sheep cheese. Additionally, it investigates the presence of virulence genes, resistance genes, and toxins in reference genomes. The main steps were (a) sample preparation and fractionation; (b) physicochemical analysis; (c) analysis of the free fatty acids profile by GC-FID; (d) analysis of the volatile compounds profile by GC-MS; (e) molecular analysis—Next Generation Sequencing of the 16S rRNA gene (V3-V4 region); and (f) in silico analysis—Genomics. A total of 1,061,392 sequences were identified, corresponding to 45 genera and 57 species. Of the total abundance, 95.7% were considered beneficial, while 3.9% were classified as bacteria with pathogenic potential (BPP) and/or bacteria harmful to milk technology (BHMT). Five phyla were identified: Firmicutes, Proteobacteria, Actinobacteriota, Bacteroidota, and Fusobacteriota. The genera Acinetobacter, Pseudomonas, and Staphylococcus stood out in the BPP and BHMT groups, showing higher abundance. Alpha diversity of the cheese samples showed that the cheese origin significantly influences the richness, evenness, and abundance of bacterial species. Some physicochemical parameters, fatty acids, and volatile organic compounds showed a negative correlation with Staphylococcus. Reference genomes of two species exhibited a higher number of resistance and virulence genes. This reinforces the need to monitor bacteria considered of lesser relevance to prevent the transmission, through food, of potentially resistant and virulent pathogens. [ABSTRACT FROM AUTHOR]