With the death of President Roxas, Quirino assumed the presidency on April 17, 1948. He was elected president the next year, and served a full term until December 1953.

In July 1953, he extended Executive Clemency to the remaining prisoners of war (POW) still incarcerated in Muntinlupa, sending back the Japanese POW to Japan. This act of Christian forgiveness earned Quirino the respect and trust of the Japanese nation.

The former president died in retirement at his residence in Novaliches, Quezon City on February 29, 1956.