The purpose of this study was to identify barriers to accessing sexual health services among gay, bisexual and heterosexual-identifying men who have sex with men and male-to-female transgender persons in Guatemala City, to inform the development of high quality and population-friendly services. In-depth, semi-structured interviews were conducted with 29 purposively sampled individuals, including 8 transgender, 16 gay/bisexual and 5 heterosexual-identifying participants. Topical codes were applied to the data using software Atlas.ti™ to compare data between sub-groups. Analysis revealed that public clinics were most commonly used due to their lower cost and greater accessibility, but many participants experienced discrimination, violation of confidentiality and distrust of these services. Transgender and gay/bisexual-identifying participants preferred clinics where they felt a sense of belonging, while heterosexual-identifying participants preferred clinics unassociated with the men who have sex with men community. The most prominent barriers to sexual health services included fear of discrimination, fear of having HIV, cost and lack of social support. Findings highlight the need to strengthen existing public sexually transmitted infection clinics so that they address the multiple layers of stigma and discrimination that men who have sex with men and transgender persons experience.