Shifting agricultural soil ecosystem represents stress of varying degrees depending upon the length of the fallow cycle. In this study, we try to assess the synergistic effect of microbial diversity on different rhizospheric niches (loosely adhered and strongly adhered rhizosphere soil, bulk soil, and the crop root interior) of different fallow cycles (5, 8, and 20 years) using culture-dependent and independent approaches along with their metabolic profiling. Culture dependent study shows higher bacterial diversity in strongly adhered rhizosphere soil followed by loosely adhered rhizosphere soil (F = 156, p < 0.001) irrespective of crop type and fallow cycle length. The high-throughput 16S rRNA gene sequencing shows 5% higher bacterial diversity in 5 years than in 8 and 20 years fallow soil (p < 0.05). The community composition was significantly affected by the length of fallow periods in all rhizosphere niches, driven primarily by an increased relative abundance of Proteobacteria and Bacteroidetes in long than short fallow cycles. We have observed a selective promotion of rhizobacterial communities in different niches of low nutrient soil in the short fallow period that complies with the crop field’s bacterial metabolic pathways. Our study answers an inconclusive question on bacterial diversity dynamics in shifting field crop rhizosphere and soil, highlighting the predominant role of the bacterial community in the crop grown in a stressed soil system. This study may provide a scientific roadmap in developing microbial inoculum for better crop performance in nutrient-poor soil.