Monitoring key populations' progress towards UNAIDS 90-90-90 targets is essential to achieving HIV/AIDS epidemic control. Using serial cross-sectional data, we evaluated changes in HIV care continuum among people who inject drugs(PWID) and men who have sex with men(MSM) in India. Cross-sectional baseline (2012/2013) and follow-up (2016/2017) samples were recruited using respondent-driven sampling across 21 cities. All participants were tested for HIV and RNA measured in HIV-positive participants. Linear regression was used to model temporal site-level changes in continuum indicators in MSM versus PWID. At baseline, we recruited 2,544 HIV-infected PWID and 1,086 HIV-infected MSM. At follow-up, we recruited 2,517 HIV-infected PWID and 1,763 HIV-infected MSM. At baseline, there were no significant differences in continuum indicators between MSM and PWID. At follow-up, compared to PWID, the proportion of MSM reaching each care continuum indicator-awareness of status, receipt of care, ART use, viral suppression-increased by 15-33 percentage points: 78% of MSM versus 49% of PWID were aware of their status ( < 0.01); 56% of MSM versus 32% of PWID were virologically suppressed ( = 0.05). MSM showed marked improvements across the care continuum, whereas PWID lagged and may require additional intervention. Differential improvement in HIV engagement may necessitate population-specific interventions and routine surveillance to facilitate HIV elimination.