This research concerns the influence of contrasting tillage practices (Zero Tillage (ZT), Permanent Bed (PB) and Conventional tillage (CT)) in main plots and crop rotation (rice-wheat (R-W), rice-maize (R-M) and rice-lentil (R-L)) under rice based cropping system under split plot design with three replication, on soil microbial budgeting in terms of size and structure of microbial population, dehydrogenase activity (DHA), phosphatase activity and fluorescein diacetate (FDA) hydrolysis. Rice base cropping system is advocated as the dominant system prevailing in India due to the better suitability to its landforms and climatic conditions. Within tillage system, SOC was reported higher in zero tillage (0.67%), compared to permanent bed planting (0.66%) and CT (0.62%) at 0-15cm. At 15-30cm depth, zero tillage (0.57%) and PB (0.58%) registered significantly (P < 0.05) higher SOC compared to CT (0.52%). In this study, we estimated the microbial community size and structure, enzymatic activities, mychorrizal root infection and soil organic carbon (SOC). Root and rhizospheric soil samples were collected during two consecutive seasons from a 5 year old long term field experiment on conservation agriculture located at Research farm, Bihar Agricultural College, Sabour and still continuing. ZT treatment resulted higher soil organic carbon content (0.57%), viable microbial population (19.6% higher fungi, 10.63% bacteria, and 12.6% actinomycetes), dehydrogenase activity (5.3-9.11%), phosphatase activity (9.3-10.57%) which was at par with PB and differed significantly to that of CT treatment. Thus tillage practices and crop diversifications are the important factors affecting soil microbial community size and structure.