An invitation from state health officials spurred Puente to begin conducting public health and community development programs corresponding to student research. After two summers as a student-run program, Puente began operating year-round as a project of the Houston Advanced Research Center in March 2003.

In June 2004, Puente received its 501(c)(3) status and now operates as a U.S. public charity. Puente also has Mexican charity status as an Asociación Civil, which was granted in November 2005.