In 1932, he became an Associate Justice of the Supreme Court. He became its Chief Justice on December 24, 1941. As part of the emergency reorganization of the Commonwealth government, Abad Santos, in his capacity as Chief Justice, was given the responsibilities previously handled by the Secretary of Justice (the position of Secretary of Justice was abolished for the duration of the war). Abad Santos accompanied the Commonwealth government to Corregidor, where on December 30, 1941, he administered the oath of office to President Quezon and Vice-President Osmeña for the second term they'd been elected to in November of that year. He also undertook, with Manuel Roxas, the supervision of the destruction of Commonwealth government currency to prevent its falling into enemy hands. With the Japanese invasion rapidly advancing to the southern part of the Philippines, President Manuel L. Quezon was advised by General Douglas MacArthur to establish a government in exile to the United States, Quezon invited Chief Justice Abad Santos to leave with him. The latter declined preferring to remain in the Philippines and carry on his work and stay with his family. On March 17, 1942 the day of Quezon's departure at Zamboanguita, Negros Oriental for the US by way of Australia, he appointed Abad Santos as the Acting President with full authority to act in the name of, and on behalf of the President of the Commonwealth of the Philippines and become the Acting Commander-in-Chief of the Armed Forces of the Philippines in some areas unoccupied by the Japanese. On April 11, 1942, Abad Santos, his son José Jr. (nicknamed "Pepito"), Col. Benito Valeriano and two enlisted men were captured by the Japanese in barangay Tubod in Barili, Cebu while traveling by automobile to Toledo, Cebu. He identified himself as the Chief Justice of the Supreme Court of the Philippines. He and his son were then taken to a concentration camp in Basak San Nicolas, Cebu City. When asked to cooperate with the Japanese, he refused. Although he had nothing to do with military operations, they imputed to him, as acting president, the destruction of the bridges and other public works in Cebu that had been undertaken by the USAFFE forces to delay the invasion of the island. The Japanese High Commander Kiyotake Kawaguchi took him and his son aboard a ship on April 26, 1942, thinking they were heading to Manila. Instead, they arrived on April 28 at Parang, Cotabato (now in Maguindanao).