Yogurt is a widely consumed traditional fermented food. The health benefits and shelf life of yogurt depend on the type and magnitude of fermenting microorganisms, the proportion of physicochemical parameters, and the presence of microbial and metal contaminants. This study aimed to investigate the physicochemical properties and bacterial diversity of sour and sweet yogurts, commercially and locally produced in Bangladesh. A total of 38 samples, 19 each for sour and sweet yogurts, randomly collected from several commercial and local brands in Bangladesh. The most standard AOAC methods were used to perform proximate analysis, AAS to determine minerals, and high-throughput Illumina sequencing of 16S rRNA genes to conduct metagenomic analysis. For statistical and bioinformatic analysis, R and QIIME 2 were used, respectively, to perform OTU extractions and rarefaction, alpha and beta diversity, and spearman correlation. Sweet yogurts contained significantly greater pH, fat, moisture, TS, SNF content (%, w/w) and Streptococcus spp.(%) than sour samples, whereas sour yogurts contained more moisture, ash, minerals content (Zn, Na, Ca and Mg) and Lactobacillus spp. (% ). Sour samples had more bacterial diversity, along with probiotics and potentially harmful opportunistic path-ogens, including Enterobacter, Lactococcus, Aeromonas and Acinetobacter. Also, commercial brands exhibited higher abundance of some well-known probiotic strains than the local brands. The more the ash content, the more amount of Ca was exhibited. The relative abundance of most of the bacterial genera, except Lactobacillus, was positively correlated with each other. Except for Lactobacillus, fat (%) had negatively, whereas pH and moisture had positively influenced the growth of other bacterial genera. The presence of Hafnia in yogurt positively influenced the bioavailability of all minerals (Fe, Zn, Cu, Na, k, Ca and Mg). Nutritional parameters were varied based on the taste of yogurt samples with sour ones having greater nutritional values and bacterial diversity. These findings would help understand in consuming yogurts for health benefits.