Before the Spaniards the islands had their own fermented drinks: tuba (palm wine), basi, tapuy and the distilled lambanog. Beer came with the Spanish ships, and by the 1880s the rich of Manila bought it from Europe; José Rizal lists European beer among their purchases in Noli me tangere (1887). In 1889 Enrique María Barretto de Ycaza, a Manila-born businessman, applied for a royal grant from Spain to brew beer in the colony and received it for twenty years. La Fábrica de Cerveza San Miguel opened in 1890 (29 September in the company's account, 4 October on the 1950 historical marker) at 6 Calzada de Malacañang in the San Miguel district of Manila, with an ice plant beside the brewhouse. It is often said that this was the first brewery in Southeast Asia, but no source confirms it, and some lists date a Saigon brewery to 1875.

The firm was incorporated in 1893, with Pedro Pablo Róxas as manager and the German brewmaster Ludwig Kiene, who made the Pale Pilsen from Bohemian malt and hops. It won its first prize at the Exposición Regional de Filipinas in 1895 and by 1896 sold more than five bottles for every imported one. In 1913 it became San Miguel Brewery, Inc. and in 1914 began to export to Hong Kong, Shanghai and Guam. A Manila syndicate led by Antonio Barretto, a cousin of the founder, had the Oriental Brewery of Hong Kong re-erected at Nagtahan in 1913; San Miguel bought it out in 1919 and made it an ice plant, later the Royal soft drinks plant.

The Japanese-owned Balintawak Beer Brewery opened at Polo, Bulacan (now Valenzuela), in the mid-1930s with Mitsui Bussan money. In the war years of 1942-45 it and the Manila plant brewed for the Japanese forces, and in 1947 San Miguel under Andrés Soriano moved its brewing to Polo; the old Manila buildings were pulled down later and the site became part of the Malacañang grounds. In 1953 San Miguel licensed its name to a Spanish company that brewed San Miguel in Spain from 1957. A brewery at Mandaue, Cebu, started in 1968.

San Miguel had no large rival until 27 January 1982, when Lucio Tan opened Asia Brewery at Cabuyao, Laguna, with Beer Hausen Pale Pilsen. San Miguel answered with Lagerlite, Red Horse and Gold Eagle; Asia Brewery with Max, Manila Beer, Carlsberg under licence from 1987 and, in 1988, a cheap 'Beer Pale Pilsen', now Beer na Beer. San Miguel sued in September 1988 over the label; the Court of Appeals found for it in 1991, but on 5 July 1993 the Supreme Court ruled for Asia Brewery. San Miguel's beer business became San Miguel Brewery, Inc. on 1 October 2007; in 2009 Kirin Holdings of Japan bought 43.25% of it from the parent and more by tender offer, reaching 48.3%. San Miguel's market share was 88% in 2011 and about 95% in 2019.

In 2016 Asia Brewery and Heineken agreed to form AB Heineken Philippines to brew Heineken at Cabuyao and at El Salvador, Misamis Oriental (its second brewery since 1992); in 2026 Asia Brewery sells Heineken, Heineken Silver, Asahi Super Dry and Leon Extra Strong. In 2019 San Miguel brewed at Valenzuela, Pampanga, Mandaue, Davao del Sur and Bacolod, and in September it broke ground for a one-million-hectolitre brewery at Leganes, Iloilo. Craft beer began in the early 2010s: Katipunan Craft Ales sold its first bottle in Manila in July 2012, Palaweño Brewery opened at Puerto Princesa in 2013, and Engkanto Brewery started in Makati in 2017 and moved to Carmona, Cavite, so it was not the first. In March 2026 San Miguel opened a museum at the Polo Brewery with the royal patent of 1890.