Phelan was a progressive supporter of the policies of Woodrow Wilson and was a leader in the movement to restrict Japanese and Chinese immigration to the United States.

[6] He remained active in the anti-Japanese movement after leaving office, securing then-presidential candidate Woodrow Wilson's support for restricting Japanese immigration in 1912 and helping to push through California's discriminatory alien land law in 1913.

He concluded that American progress would be stunted if the United States continued to allow Chinese immigrants to remain in the country, and that the Chinese workers were taking work away from white workers because they worked for so much lower wages and an accustomed lower standard of living, allowing their labor to be exploited unfairly, driving down conditions of labor and standards of living generally.

"[11] Phelan's plans for the region included publicly funded water and electricity for a geographical entity he called "Greater San Francisco.

"[13] During his tenure as the Mayor of San Francisco, Phelan and his administration were faced with dealing with the plague of 1900–1904 that infected the city's Chinatown community.

On October 25, 1897, Phelan addressed the California health board in San Francisco and stated that government intervention was needed in order to establish healthier living conditions.

[14] Shortly after, the health board members were released from their duties due to political in-house fighting and excessive patronage.

In June 1900 San Francisco's city hall received the news that Joseph J. Kinyoun had instituted a travel ban in hopes of preventing the spread of the plague to the rest of the country.

[16] In order to improve sanitary living conditions in Chinatown, Governor Henry Gage proposed to hire inspectors and workers to eradicate the plague.

"During his final address before leaving office, Phelan praised the health board, claiming that because of its vigilance the city 'was saved from Oriental infection.'"

Although the San Francisco Plague in Chinatown was reported in journalism, the material printed was prone to exaggerations, biased information, and focused on making the Chinese population look substandard.

Acts of racism were apparent because publications were heavily inclined to use offensive images and headlines to attract attention of readers.

[19] During the 1906 San Francisco earthquake Phelan was a member of the Committee of Fifty, called into existence by Mayor Schmitz to manage the crisis.