In the early years, San Diego Habitat was a cross-border affiliate. Half of its leadership was in Mexico and half in the United States. Funds were raised primarily through churches and donations were small, but many. In the summer of 1987, in a bi national meeting at the Autonomous University of Baja California, approximately 50 people representing many constituencies expressed their strong support for the idea of starting a Habitat affiliate in the San Diego-Tijuana region. This bi-national affiliate was to become the only one of its kind in the history of Habitat and was designed from the beginning to create a cross-border partnership for working together on the lack of affordable housing throughout the metropolis of Tijuana, Mexico and San Diego, California.
In January 1988, the San Diego-Tijuana Habitat for Humanity was officially approved and incorporated in California as a 501(c)(3) non-profit corporation.