With Serra's death, Palóu became the acting "presidente" of the Upper California missions until the formal appointment of Lasuén as successor to Serra. Palou remained at Mission San Carlos until failing health and old age led him to retire in 1785 to the missionary College of San Fernando de Mexico. He was elected guardian of the college and held this office until his death in Mexico, where he had completed his biography of Serra, most of which he had written while still in California.