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Background: Chronic musculoskeletal (MSK) diseases are an important cause of disability in the Mayan community of Chankom in Yucatán, Mexico., Objective: To understand a community-based participatory research (CBPR) strategy implemented in Chankom to design a community-based rehabilitation (CBR) program for people living with MSK diseases., Methods: Qualitative descriptive thematic analysis from an ethnographic work conducted in Chankom, during the implementation of a CBPR strategy from 2014 to 2017., Results: Four main themes describe the main processes that formed our CBPR strategy: 1) forming and maintaining an alliance between academic and community members, 2) prioritizing community needs, 3) integrating local and global knowledge and 4) shared-decision-making. This CBPR strategy allowed the design of a CBR program formed by six main interventions: 1) health services coordination, 2) personal support, 3) community venous blood sampling services, 4) community specialized services, 5) health promotion, and 6) health transportation services., Conclusions: Co-designing a CBR program for people living with chronic MSK diseases in Chankom was possible through an extensive community engagement work structured around four main processes, including the essential principles of CBPR. The designed CBR program includes culturally sensitive interventions aimed at improving the quality, availability, accessibility, and acceptability of health care services. Moreover, the program mainly addressed the "health" component of the World Health Organization-CBR matrix, suggesting a need for a new CBPR cycle after it is implemented and evaluated in the future.