Female sex workers (FSWs) may benefit from pre-exposure prophylaxis (PrEP) including microbicides for HIV prevention. Since adherence is a key factor in PrEP efficacy, we explored microbicide acceptability and potential barriers to use within FSWs' intimate relationships in Tijuana and Ciudad Juárez, Mexico, where HIV prevalence is increasing. FSWs and their verified intimate (non-commercial) male partners completed quantitative and qualitative interviews from 2010 to 2012. Our complementary mixed methods design followed an iterative process to assess microbicide acceptability, explore related relationship dynamics and identify factors associated with concern about male partners' anger regarding microbicide use. Among 185 couples (n=370 individuals), interest in microbicides was high. In qualitative interviews with 28 couples, most participants were enthusiastic about microbicides for sex work contexts but some explained that microbicides could imply mistrust/infidelity within their intimate relationships. In the overall sample, nearly one in six participants (16%) worried that male partners would become angry about microbicides, which was associated with higher self-esteem among FSWs and lower self-esteem and past year conflicts causing injury within relationships among men. HIV prevention interventions should consider intimate relationship dynamics posing potential barriers to PrEP acceptability and adherence, involve male partners and promote risk communication skills.