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The bacteria harboring <i>phoD</i> encodes alkaline phosphatase (ALP), a secretory enzyme that hydrolyzes organic phosphorous (P) to a usable form in the soil. The impact of farming practices and crop types on <i>phoD</i> bacterial abundance and diversity in tropical agroecosystems is largely unknown. In this research, the aim was to study the effect of farming practices (organic vs. conventional) and crop types on the <i>phoD</i>-harboring bacterial community. A high-throughput amplicon (<i>phoD</i> gene) sequencing method was employed for the assessment of bacterial diversity and qPCR for <i>phoD</i> gene abundance. Outcomes revealed that soils treated for organic farming have high observed OTUs, ALP activity, and <i>phoD</i> population than soils managed under conventional farming with the trend of maize > chickpea > mustard > soybean vegetated soils. The relative abundance of <i>Rhizobiales</i> exhibited dominance. <i>Ensifer</i>, <i>Bradyrhizobium</i>, <i>Streptomyces</i>, and <i>Pseudomonas</i> were observed as dominant genera in both farming practices. Overall, the study demonstrated that organic farming practice favors the ALP activity, <i>phoD</i> abundance, and OTU richness which varied across crop types with maize crops showing the highest OTUs followed by chickpea, mustard, and least in soybean cropping.