Due to the alarming effect of synthetic and chemical-based agriculture on human health and the environment, organic farming has been receiving increasing attention around the world. Panchagavya (PG) and farmyard manure play crucial roles in organic farming’s nutrient management. Despite its known potential in crop applications, Panchagavya microbial profile has yet to be mapped. The aim of this study is to unveil the succession of bacterial communities in Panchagavya during the fermentation process using targeted amplicon analysis. The results revealed that 45 phyla, 92 classes, 168 orders, 333 families, 899 genera, and 2026 species were obtained from all samples, along with 5144 OTUs. Proteobacteria (36.61-70.98%) and Bacteroidetes (14.59-23.81%) were found in greater abundance in all samples, with Proteobacteria being the most common in all samples, followed by Bacteroidetes and Firmicutes (12.67-29.58%). Pseudomonas was a dominant member of the fermentation process, along with Romboutsia, Paeniclostridium, Clostridium, Enterococcus, Lactobacillus, Bifidobacterium, and Ruminococcus. The findings indicate that Panchagavya demonstrates effectiveness as a fertilizer due to its inclusion of advantageous microorganisms and growth stimulants for plants. Furthermore, some bacterial members that have not yet been characterized for any role in the soil and plant systems, urging a comprehensive investigation into the potential functions for future agricultural applications and practices.