Yogurt, a popular fermented food, relies on fermenting microorganisms, physicochemical parameters, and contaminants for its health benefits and shelf life. This study investigated sour and sweet yogurts in Bangladesh, analyzing 38 samples using standard methods like AOAC for proximate analysis, AAS for mineral determination, and Illumina sequencing for metagenomic analysis. Sweet yogurts had higher pH, fat, moisture, total solids (TS), solid-not-fat (SNF) content, and Streptococcus spp. Sour yogurts contained more moisture, ash, and minerals (Zn, Na, Ca, and Mg), and Lactobacillus spp. Sour yogurts showed greater bacterial diversity, including probiotics and potential pathogens like Enterobacter, Lactococcus, Aeromonas, and Acinetobacter. Commercial brands had more probiotic strains than local ones. Ash content positively correlated with Ca levels. Other bacterial genera, except Lactobacillus, correlated positively with each other, with fat content negatively affecting them. Hafnia presence in yogurt positively impacted mineral bioavailability. Nutritional values varied, with sour yogurts having higher values and bacterial diversity. Pathway analysis revealed sour yogurts' association with bacterial chemotaxis, peptidoglycan biosynthesis, and Vancomycin resistance, while sweet yogurts showed beta-lactam resistance. This underscores the nutritional and microbiological advantages of sour yogurts, guiding production and consumption choices for better health.