Background: Condomless anal intercourse (CAI) appears to be increasing among men who have sex with men (MSM) globally, and is reported to be as high as 70% in recent studies in Peru. To improve understanding of the evolving context of CAI among MSM in Peru, we studied associations between partner type, substance use, and condomless anal intercourse (CAI) in locations where MSM commonly report having sexual encounters. Methods: In a 2017 cross-sectional study of rectal STI screening and HIV prevention, a convenience sample of MSM recruited from community venues in Lima completed a survey of demographic characteristics and sexual risk behavior with their three most recent partners. Generalized estimating equations estimated correlations of CAI with location of last sexual contact, participant substance use prior to sex, and negotiation of condom use before or during sex. The network data integration application, Cytoscape, mapped intersections of partner type, sexual orientation, substance use, and CAI by four types of locations where sex occurred: 1) Home, 2) Hotel, 3) Sauna or Internet Cabin, and 4) Public Spaces. Results: Of 447 MSM (median age 27 years), 76.9% reported CAI with ≥1 of their last three partners. Participants reported sex with casual partners most commonly in homes (64.6%) and hotels (60.4%), and with anonymous partners most often in saunas/Internet cabins (57.5%) and public spaces (52.6%). CAI was less commonly reported in hotels (aPR, 95% CI: 0.85, 0.75-0.97) compared to homes. Participants who used marijuana before sex at home were more likely to report CAI than MSM who did not use marijuana (1.36, 1.01-1.92). Partner alcohol use before sex was associated with CAI in saunas/Internet cabins (3.17, 1.45-6.91) and public spaces (2.65, 1.41-4.98). In the sexual network maps, almost all MSM who used drugs prior to their sexual encounters used drugs with more than one of their last three partners. Conclusions: CAI was common and associated with different risk factors, like partner type and substance use, based on location where sex occurred. Novel combination HIV, STI, and substance use prevention interventions must consider how the social environments of MSM influence condom use and other sexual risk behaviors. Trial registration: ClinicalTrials.gov Identifier NCT03010020, January 4, 2017.