Beejamrit is an ancient organic formulation commonly used as a seed treatment in organic and natural farming in India. This low-cost input is primarily composed of cow dung, cow urine, and forest soil, which is often supplemented with limestone. In organic agriculture, it is a traditional practice among the farming community to incubate the seeds in Beejamrit prepared overnight before sowing in the field. However, a lack of substantial scientific evidence has been a major limitation to promote this farmers' innovative practice. On the other hand, growing data suggests that cow-based formulations are mostly enriched with microbial sources, including several plant growth-promoting rhizobacteria that are capable of synthesizing plant growth regulators. However, the microbiological properties of Beejamrit and their temporal changes over different periods of decomposition are largely unexplored. In this study, we aim to analyze the decomposition rate of Beejamrit over 7-consecutive days of incubation. This study further elucidates the microbial niche and their dynamics in Beejamrit, including the plant-beneficial bacteria. It was observed that the population of plant-beneficial bacteria such as the free-living nitrogen fixers and the phosphate solubilizers proliferates progressively up to 4-days of incubation. Similarly, the indolic compounds, including indole acetic acid, were enriched to the highest concentration in Beejamrit after 4-days of decomposition. Together, our analyses establish that Beejamrit provides a dynamic, microbe-based metabolic network and acts as a plant growth regulator. In conclusion, this study recommends the Beejamrit preparation after 4-days of incubation in the seed treatment and foliar spray to receive its optimum benefits.