When the Jesuits were expelled from Baja California and the Franciscans and the government of New Spain assumed responsibility for the peninsula in 1768, Velásquez was promoted to the rank of corporal.
At Monterey in 1770 he was dispatched south with documents, travelling overland as far as southern Baja California Sur and from there to San Blas and Mexico City.
An important part of Velásquez' duties was to locate potential sites for Dominican missions in the frontier zone between Velicatá and San Diego.
In July 1781, the Quechan Indians on the lower Colorado River rose in revolt and killed Hispanic missionaries, settlers, and travelers.
In 1783 Velásquez led an exploratory party that reconnoitered the backcountry east of San Diego for a possible more direct route to the lower Colorado River.