The efficacy of Pseudomonas putida (GN1) and Burholderia cepacia (KKM1) as seed treatment and soil application along with neem cake against groundnut root rot and stem rot disease was evaluated under rainfed conditions during the years 2021, 2022 and 2023. The present study is to evaluate biocontrol agents and organic amendments against Macrophomina phaseolina and Sclerotium rolfsii in peanut. The result showed that neem cake (10 %) recorded the maximum inhibition of Macrophomona phaseolina (40.91 %) and S. rolfsii (45.45 %) under in vitro whereas neem cake combined with P. putida and B. cepacia as seed treatment 10 g/kg of seed and soil Application of P. putida @ 2.5 kg + Neem cake 150 kg/ha decreases the soil-borne diseases of root rot (71.70 %) and stem rot (64.88 %) and also increased the yield 2130.48 kg/ha with the cost-benefit ratio of 2.74 under rainfed field conditions comparing to other treatments. In addition, the same treatment increased the total root length (2110.41 mm), Root tips (573 Nos), forks (501 Nos), Maximum diameter (18.11 mm) and estimated volume (27170 cm3 ) when using BioVis PSM Root -Rhizoscanner.