President Quezon died in exile in Saranac Lake, New York on August 1, 1944. Sergio Osmena became President of the Philippine Commonwealth and came ashore at Leyte with MacArthur.
Osmena's Nacionalista Party had split with Manuel Roxas leading the newly formed Liberal Party. Roxas had served in Laurel's government and a bitterly divisive election campaign centered on his conduct during the war. Roxas won the election on April 23, 1946 to become the first President of Republic of the Philippines on July 4, 1946.
Relations between the Republican government and the Hukbalahap were confrontational and often violent in the post-war years, especially as landlords returned to reclaim the estates they had abandoned during the occupation. Roxas was in turns conciliatory and repressive in his dealings with the Huks. In 1948 he extended a general amnesty to all those arrested for collaboration with the Japanese and, in the same year, declared the Huks a subversive and illegal organization.
Roxas died of a heart attack in April 1948 and was succeeded by Elpidio Quirino. Quirino attempted to negotiate with the Huk leader Taruc but the effort came to nothing. Huk strength reached its peak with as many as 15,000 armed men during and for a time following the 1949 presidential election campaign. Quirino and the Liberals were returned to office.
Quirino's Secretary of Defense, Ramon Magsaysay, succeeded in his policy to put down the Huks militarily and gain popular support for the civil authority. He imposed strict discipline on the military police to restrain their abuses of civilians. At the same time, the Huks lost their popular support through their indiscipline. Many had become nothing more than common robbers and bandits. The Huks finally lost the sympathy and respect of the people with the murder of President Quezon's widow and her family.
Magsaysay ran for the Nacionalista Party in 1953 and took two-thirds of the vote to defeat Quirino. Magsaysay enjoyed a popular presidency. He started many small but important local projects building roads, bridges, wells and irrigation canals. He established special courts to resolve landlord-tenant disputes. Taruc surrendered to the government in May 1954 signalling the decline of the Huk threat.
Carlos Garcia became President when Magsaysay died in an airplane crash on March 17, 1957. Garcia was reelected President in 1957 in the warm afterglow of Magsaysay's popularity. The Liberal Party recovered its strength under Diosdado Macapagal who won the 1961 presidential election.
Soon after taking office, President Macapagal proclaimed June 12 a national holiday in celebration of Philippine Independence. General Emilio Aguinaldo, who first proclaimed Philippine Independence on June 12, 1898, was the guest of honour at the first Independence Day celebrations held on June 12, 1962.