Implementing health information technology (IT) at the community level is a national priority to help improve healthcare quality, safety, and efficiency. However, community-based organizations implementing health IT may not have expertise in evaluation. This study describes lessons learned from experience as a multi-institutional academic collaborative established to provide independent evaluation of community-based health IT initiatives. The authors' experience derived from adapting the principles of community-based participatory research to the field of health IT. To assist other researchers, the lessons learned under four themes are presented: (A) the structure of the partnership between academic investigators and the community; (B) communication issues; (C) the relationship between implementation timing and evaluation studies; and (D) study methodology. These lessons represent practical recommendations for researchers interested in pursuing similar collaborations.