Soil microbes play critical roles in soil biogeochemistry, soil biological health and crop productivity.  The current study evaluated the effects of tillage and residue management on changes in soil biochemical indicators at different growth stages of wheat after 5 years of rice-wheat system.  Nine treatment combinations of tillage, crop establishment and crop residue management included three main plot treatments applied to rice: (1) conventional till direct dry seeded rice (CTDSR), (2) zero till direct dry seeded rice (ZTDSR), and (3) conventional puddled manual transplanted rice (CTPTR) and three sub-plot treatments in subsequent wheat: (1) conventional tillage with rice residue removed (CTW-R), (2) zero tillage with rice residue removed (ZTW-R) and (3) zero tillage with rice residue retained as surface mulch (ZTW+R).  Irrespective of rice treatments, ZTW+R treatment had higher soil biochemical indicators compared with ZTW-R and CTW-R at all the growth stages of wheat.  Generally, all the biochemical indicators were the highest at the flowering stage of wheat.  Residual effect of rice treatments was also significant on biochemical quotients in wheat, which were the highest under ZTDSR followed by CTDSR and CTPTR.  The present study provided three sensitive and reliable biochemical indicators (microbial biomass, basal soil respiration and microbial quotient) which respond rapidly to change in tillage and residue management practices in RWS of South Asia.