This case study involves the experiences of researchers conducting community-based research during the Recharge@Work intervention to reduce sedentary behavior in desk-dependent office workers. Recharge@Work was a community-based research study consisting of a multicomponent, theory-based intervention conducted at two large hospitals in the Northwest United States. The aims were to (a) investigate psychosocial and organizational correlates of sedentary behavior in an occupational setting and (b) evaluate an intervention to reduce sedentary behavior in the same occupational setting. Working with three organizations and finding a balance between strong research methodology and the needs of community partners created many challenges. The complexity of a theory-based intervention as well as logistics of data collection and evaluation of the program required the research team to be adaptable and flexible in designing, implementing, and evaluating the sedentary behavior intervention. This case study discusses the specific challenges faced when conducting a multisite behavior change intervention as well as recommendations for future research in this area of public health.