By 1700, when the threat of attack by rival tribes had diminished and perhaps under pressure from the Spaniards, the people of San Felipe relocated again to their present site at the foot of Black Mesa. This site was better suited for agriculture, rather tham atop the arid mesa.

The Pueblo was built using Spanish Colonial models, with a central plaza bordered by flat-roofed adobe houses. Unlike the multi-tiered housing seen at the nearby pueblo of Kewa, the housing at San Felipe are uniform one- and two-story structures, some with outdoor porticos that reinforce the similarities to Spanish Colonial architecture.

Adopting this model was practically syncretic because the layout aligned to the four sacred directions of the Keres: the corners of the plaza are oriented north, west, south, and east, and the corner facades are painted in the corresponding Keresan colors of yellow (north), blue (west), red (south), and white (east). The plaza is slightly sunken and used for dances, while it is framed by Black Mesa to the west and the village’s two principal communal spaces, the circular Pumpkin Kiva and Turquoise Kiva, to the north and east.