Risk perception and health behaviors result from individual-level factors influenced by specific partnership contexts. We explored individual- and partner-level factors associated with partner-specific perceptions of HIV/STI risk among 372 HIV/STI-positive MSM and transgender women (TW) in Lima, Peru. Generalized estimating equations explored participants’ perception of their three most recent partner(s) as a likely source of their HIV/STI diagnosis. Homosexual/gay (PR = 2.07; 95 % CI 1.19–3.61) or transgender (PR = 2.84; 95 % CI 1.48–5.44) partners were more likely to be considered a source of infection than heterosexual partners. Compared to heterosexual respondents, gay and TW respondents were less likely to associate their partner with HIV/STI infection, suggesting a cultural link between gay or TW identity and perceived HIV/STI risk. Our findings demonstrate a need for health promotion messages tailored to high-risk MSM partnerships addressing how perceived HIV/STI risk aligns or conflicts with actual transmission risks in sexual partnerships and networks.