Background Latino men who have sex with men (MSM) experienced a 13% increase in HIV diagnoses from 2010 to 2014, more than any other racial/ethnic subgroup of MSM in the United States. If current HIV diagnoses rates persist, about one in four Latino MSM in the United States will be diagnosed with HIV during their lifetime. Although some efficacious HIV prevention interventions for Latino MSM exist, none have focused on couples. This paper describes the protocol of a randomized controlled trial (RCT) to test the preliminary efficacy of a couple-based HIV prevention intervention that is culturally tailored for Latino men and their same-sex partners. Methods The RCT will determine the preliminary efficacy of Connecting Latinos en Pareja (CLP) to increase the proportion of anal sex acts that are HIV protected (i.e., anal sex acts in which condoms, pre-exposure prophylaxis (PrEP), treatment as prevention (TasP), or a combination thereof, are used to reduce risk of HIV transmission). CLP builds upon previous couple-based interventions with white and black MSM by incorporating biomedical prevention techniques, such as PrEP and TasP, implementing a framework responsive to the couple’s serostatus, and addressing the socio-cultural factors that influence HIV risk among Latino MSM. We also include input from community stakeholders, members of the target population, and a community advisory board as part of intervention development. Assessments will be conducted at baseline, and 3- and 6-months post-intervention to examine the intervention effects on outcomes (HIV-protected sex acts), and factors potentially mediating or moderating intervention effects. Discussion This paper describes an innovative RCT that incorporates multiple HIV prevention techniques for Latino MSM in couples, regardless of serostatus. The ongoing involvement of community stakeholders, members of the target population, and a community advisory board is emphasized, and plans for widespread dissemination and application of findings into practice are discussed. Trial registration Trial registration: NCT03048838. Registered on 3 February 2017. Electronic supplementary material The online version of this article (10.1186/s13063-018-2582-y) contains supplementary material, which is available to authorized users.