Fages was born in Guissona, Lleida province, Catalonia, Spain. In 1767, Lieutenant Fages left Spain with the Free Company of Volunteers of Catalonia for New Spain, to serve under Domingo Elizondo in Sonora. In 1769, Fages was selected by Viceroy José de Gálvez to lead the shipborn portion of the Gaspar de Portolà led expedition to found San Diego, California. Fages sailed from La Paz on January 10, 1769, aboard the San Carlos, and arrived at San Diego Bay on April 29 with scurvy-ridden troops, after sailing over 200 mi (320 km) off course because of cartography errors. Fages accompanied the 1769 and 1770 land expeditions to locate Monterey Bay. During this time he was promoted to captain.
After Portolà left California in 1770, Fages served as the somewhat independent military governor of California Nueva (New California), which was later to become Alta California, headquartered in Monterey. During this time, Fages explored by land San Francisco Bay, San Pablo Bay, the Carquinez Strait, the San Joaquin River, and surrounding areas; and earned his nickname El Oso while hunting bears near San Luis Obispo. Fages quarreled with Father Junípero Serra, presidente of the Alta California missions, and was replaced in 1774 by Fernando Rivera y Moncada.
In 1777 Fages returned to Sonora to fight the Apaches, where he was promoted to lieutenant colonel. In 1782 he was appointed Governor of the Californias, replacing Felipe de Neve, and returned to Monterey, which had replaced Loreto as the capital of the Californias in 1777. He was promoted to colonel in 1789, and resigned his governorship in 1791. He moved back to Mexico City, where he died in 1794.
Fages married Eulalia Callis June 3, 1780 in Mexico City. She was born October 4, 1758 in Barcelona, Spain and journeyed to Mexico City with her mother and brother to join her father Agustín Callis. Her father was a Captain of a company of Spanish soldiers sent to suppress Indian rebellions. Eulalia loved fashion and believed in charity. At Mission San Carlos, she gave away her clothing after seeing the lack of clothing worn by the Indians.
Pedro Fages appears as a minor character in the 1955 film Seven Cities of Gold, which presents a fanciful and historically inacurate account of the founding of Spanish California. Lieutenant Fages is played by Mexican actor Victor Junco. In the credits, Fages' name is misspelled as "Faces.