A study was carried out to evaluate the influence of tillage-residue management, N-levels and weed management on the population of bacteria, fungi and actinobacteria in soil under rice-wheat-greengram system during 2014-15 to 2015-16 at Jabalpur, India. Results showed that tillage-residue management had significant influence on microbial properties of soil. Zero tillage with preceding crop residue retention followed in all three crops in a system markedly improved soil microorganism communities by stimulating the growth of bacteria, fungi and actinobacteria. After two years of the study, conservation agriculture based practice, i.e. zero tillage with preceding crop residue retention increased population of bacteria by 65-83%, fungi by 28-32% and actinobacteria by 22-37% compared with conventional tillage with or without preceding crop residue. No significant differences in the population of bacteria and fungi were found between N-levels in 2014-15, while significant improvement was observed in 100% recommended dose of N in 2015-16. Improvement in bacterial and fungal population due to 100% recommended dose of N was 4 and 7% over 125% recommended dose of N, respectively. There was no significant change in microbial activities due to different weed management practices. These results suggest that zero tillage with preceding crop residue retention, recommended dose of N was the best practice for improving soil biological properties under rice-wheat-greengram system.