Background and Objective: Emerging findings indicate that community-based participatory research is well positioned to improve health equity among populations with social and medical vulnerabilities, such as homeless people. However, less is known about the articulations needed to conduct research projects with and for homeless people in the complex contexts of low-threshold structures. In response, this case study aimed to describe the challenges and facilitators experienced during the data collection period (April to August 2022) of a larger participatory research project. This larger study called “Homeless people in French-speaking Switzerland and integrative medicine: Desirable? Feasible?” Aims to understand the health needs and inequities among homeless people in Switzerland. Methods: The analysis was based on field observation notes taken during 38 data collection visits to homeless people structures. This ethnographic data were analyzed through thematic analysis. Results: This study highlighted three areas of challenges: a) logistics of collecting data in structures for homeless people; b) participants’ recruitment planning; c) collecting health-related data in collective environments; and two areas of facilitators: a) iteration throughout the field experiences; b) feedback from homeless people and social workers. Findings showed that the difficulties were mainly related to the functioning of the data collection sites. To overcome these barriers and adapt strategies to successfully approach participants, it was necessary to continuously learn from experience in the field and rely on involved people’s feedback and recommendations. Conclusions: Findings suggest that ethnographic fieldwork coupled with participatory paradigm are well positioned to help face encountered challenges in this field of research. Whereas ethnographic fieldwork allowed us to achieve a deep understanding of the homeless people structure’ functioning and to identify potential problems with data collection, the participatory paradigm enabled a reliance on the expert knowledge of involved individuals and adjust strategies accordingly when necessary.