Background It is important to understand the current internet-related sexual behaviours of high-risk groups such as men who have sex with men (MSM). We designed the present study to understand the types of online/mobile apps used by MSM and male-to-female transgendered people/hijras [TGH] in Mumbai, India. We also compared the internet-related ‘partner seeking’ and ‘sexual behaviours’ in MSM and TGH in Mumbai, India. Methods This is a cross-sectional analysis of secondary data collected (April to June 2020) from 8582 MSM and 4163 TGH from five targeted intervention programmes each in Mumbai, Maharashtra, India. Data on demographics, years of association with the intervention, number and type of online/mobile apps used, sexual behaviours including partners from virtual space and non-virtual (physical) space, group sex, attending parties, mobility for sexual partners, and HIV status were collected. Results MSM were more likely to have mobile phone (88% vs 51%, p < 0.001) and internet access over the phone (78% vs 27%; p < 0.001) compared with TGH. The common apps used by MSM were Grindr (48%), Facebook (42%), and Blued (36%). MSM were more likely to have partners from virtual space (91% vs 67%; p < 0.001). A higher proportion of MSM had attended parties (28% vs 2%; p < 0.001), had group sex (16% vs 6%; p < 0.001), and were mobile for sex (25% vs 4%). MSM and TGH who had partners from virtual space were significantly more likely to report ‘missed a condom at least once during penetrative sex in the past one week’ (17% vs 12%; p<0.001). In HIV positive MSM, group sex, parties, and mobility for sex, were only in those who reported partners from the virtual space. Conclusions Internet-based interventions for MSM should be incorporated in the existing targeted intervention programme and outreach workers should be trained in virtual outreach services. Among TGH, given the low reach and use of smartphones and apps, internet-based interventions may not be such a useful option, and the existing physical targeted intervention programmes should be strengthened.