Beejamrit (BJ), Jeevamrit (JV) and Ghanajeevamrit (GV) the core inputs for practicing natural farming in India have been characterized for the plant nutrient content and microbial composition using cultural and metabarcoding techniques. Also, Phosphorus (P) solubilization efficiency of rhizosphere microbes receiving these natural farming inputs has been compared with organic, integrated and inorganically managed soils microbes. Chemical analysis revealed higher total NP and K (2.04, 0.3 and 1.3% respectively) in GV. Metabarcoding revealed dominance of Bacillota (87.5%) in JV, whereas Beejamrit and Ghanajeevamrit had abundance of Pseudomonadota with 49.67% and 46.77% OTU respectively. Higher abundance of Lactococcus, Clostridium, Lacticaseibacillus, Lactiplantibacillus and Acetobacter was found in JV. GV had higher diversity of bacteria and Flavobacterium, Hydrogenophaga, Pseudomonas and Arenimonas was dominant genera. Highest solubilization of phosphorus was observed by mixed microbial community in Control soil (CONT) 92.75 µg/mL and natural farming (NF) soil 90.56 µg/mL on 21 days of incubation (DAI) while P solubilization by bacterial flora was recorded highest in NF 40.77 µg/mL on 21 DAI followed by integrated crop management (ICM) 38.76 µg/mL and organic farming (OF) soil 34.12 µg/mL on 14 DAI. P solubilization by bacterial flora ranged from 34.36% in CONT to 67.63% in ICM. It can be concluded that organic and low input management system supported more efficient microbes in P solubilization while bacterial contribution was more where nutrient source was added exogenously.