By the 1890s, San Francisco was suffering from machine politics and corruption once again, and was ripe for political reform. Adolph Sutro ran for mayor in 1894 under the auspices of the Populist Party and won handily without campaigning. Unfortunately, except for the Sutro Baths, Mayor Sutro substantially failed in his efforts to improve the city.

The next mayor, James D. Phelan elected in 1896, was more successful, pushing through a new city charter that allowed for the ability to raise funds through bond issues. He was able to get bonds passed to construct a new sewer system, seventeen new schools, two parks, a hospital, and a main library. After leaving office in 1901, Phelan became interested in remaking San Francisco into a grand and modern Paris of the West. When the San Francisco Art Association asked him to draft a plan for the beautification of the city, he hired famed architect Daniel Burnham. Burnham and Phelan's plan was ambitious, envisioning a 50-year effort to transform the city with wide diagonal boulevards creating open spaces and squares as they crossed the orthogonal grid of existing streets. Some parts of the plan were eventually implemented, including an Opera house to the north of City Hall, a subway under Market Street, and a waterfront boulevard (The Embarcadero) circling the city.

In 1900, a ship brought with it rats infected with bubonic plague. Mistakenly believing that interred corpses contributed to the transmission of plague, and possibly also motivated by the opportunity for profitable land speculation, city leaders banned all burials within the city. Cemeteries moved to the undeveloped area just south of the city limit, now the town of Colma, California. A fifteen-block section of Chinatown was quarantined while city leaders squabbled over the proper course to take, but the outbreak was finally eradicated by 1905. However, the problem of existing cemeteries and the shortage of land in the city remained. In 1912 (with fights extending until 1942), all remaining cemeteries in the city were evicted to Colma, where the dead now outnumber the living by more than a thousand to one. The above-ground Columbarium of San Francisco was allowed to remain, as well as the historic cemetery at Mission Dolores, the grave of Thomas Starr King at the Unitarian Church, and the San Francisco National Cemetery at the Presidio of San Francisco.