This study was designed to evaluate the microbial profiling of anaerobic digestion during the processing of sewage sludge and food waste to volatile fatty acids (VFAs) in an immersed membrane bioreactor (iMBR) operating with a distinct organic loading rate (OLR). The results indicated that Firmicutes (0.17–0.38) and Actinobacteria (0.20–0.32) phyla dominated in anaerobic digestion with OLRs of 4 and 8 g VS/L/d, while Firmicutes (0.04–0.08), Actinobacteria (0.03–0.08) and Proteobacteria (0.02) were more abundant with OLR of 6 and 10 g VS/L/d in the bioreactors. Subsequently, the abundance of the Clostridium and Lactobacillus genera were responsible for higher yields of acetate, butyrate, caproate and lactate. The species of Clostridium sp. W14A (0.04–0.06), Bacterium OL-1(0.01–0.30) and Lactobacillus mucosae (0.002–0.01) were rich for both OLR dosages. Additionally, network and redundancy analysis confirmed that Clostridium sp. W14A, Bacterium MS4 and Lactobacillus had significant correlations with the VFAs produced, such as acetate, butyrate, and caproate. Variation analysis also demonstrated an appreciable correlation between environmental factors and the bacterial community. Overall, this bacterial community was dominated by the Firmicutes (0.04–0.38) phylum and Clostridium sp. W14A (0.04–0.60) species, which is a clear indicator of a lower population of acetogenic bacteria associated with greater VFAs generation.