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Comparative European data using Second Generation Surveillance System (SGSS) are scarce among gay, bisexual and other men who have sex with men. This study evaluated the implementation of Sialon II, a bio-behavioural HIV research combined with targeted HIV prevention in 13 European cities conducted in collaboration with community partners. A mixed-methods process evaluation assessed the project's coverage, outputs, quality, challenges and opportunities for improvement. Data collected through structured questionnaire from 71 data collectors from community-based organisations and semi-structured interviews with 17 managers of participating gay venues were analysed. Overall implementation was successful, achieving 4901 valid behavioural questionnaires and obtaining 4716 biological samples. Challenges in conducting bio-behavioural research in gay venues related to strict research protocols and unfavourable characteristics of venues. Formative research, collaboration with community gay venues, and offering HIV prevention emerged as facilitators. Community researchers' training was crucial for fidelity to research protocols, increased trust amongst communities and enabled data collectors to effectively address practical problems in the field. Scientifically sound SGSS with community participation is feasible and allows for including 'hard-to-reach' populations. Prevention benefits include awareness raising, capacity building and sexual health promotion in gay venues. The findings are beneficial for epidemiological research among other HIV key populations.