Background Factors influencing condom use among MSM/TW may include partner type and recent STI diagnosis. We examined the association of partner type with UAI among MSM/TW in urban Lima, Peru, recently diagnosed with HIV or STI. Methods We surveyed MSM/TW in Lima diagnosed with HIV/STI within the last month regarding their sexual practises with the most recent partner according to partner type (stable, casual, anonymous, commercial sex client or sex worker). We used a multivariate regression analysis to estimate prevalence ratios (PR) with UAI as the main outcome. Results Among 340 participants (mean age: 30.9, range: 18 – 60), 62.5% self-identified as homosexual, 5.7% heterosexual, 17.6% bisexual, and 14.3% TW. Participants classified their last partners as 44.5% stable, 34.0% casual, 10.2% anonymous, 9.9% commercial sex client and 1.5% sex worker. Overall, 72.3% of participants reported UAI with their last partner. Using stable partners as the reference category, UAI was positively associated with all other partner types: PR: 1.5 (95% CI: 1.1 – 1.9, p < 0.05) for casual partners, PR: 1.5 (95% CI: 1.0 – 2.0, p < 0.05) for anonymous partners, PR: 1.6 (95% CI: 1.2 – 2.0, p < 0.05) for commercial sex clients and PR: 2.3 (95% CI: 1.7 – 3.0, p < 0.05) for sex workers. Conclusion UAI with the last partner was more commonly reported for non-stable partners. These unexpected results warrant further investigation into the influence of partner type on high-risk sexual behaviour among HIV/STI infected MSM/TGW. A better understanding of relational partner-level factors is critical for improving HIV/STI prevention and partner notification efforts for Peruvian MSM/TGW.