Traveling to Spain in 1893, Muñoz Rivera studied the Spanish political system and was drawn to the president of the Fusion Party, Práxedes Mateo Sagasta. Following his return to Puerto Rico after the death of his father, Muñoz Rivera learned that the Autonomist Party had split into two groups, one following him and the other following José Celso Barbosa. The “Barbosistas” accused Sagasta of having ideas antithetical to their desire to establish a republic, calling him a monarchist. After the assassination of Antonio Cánovas del Castillo, Sagasta granted Puerto Rico its autonomy, comparable to that of Spanish Provinces, in December 1897. Muñoz Rivera then changed the name of the Autonomist Party to the Liberal Party of Puerto Rico and served as Secretary of Grace, Justice and Government and Chief of the Cabinet for the independent Government of Puerto Rico.
Following the American invasion and defeat of the Spanish, the signing of the Foraker Act in 1900, which established the application of American Federal law and a civilian government in Puerto Rico, dissolved the autonomous government created under the Spanish regime. Muñoz Rivera would debate against the military governors John R. Brooke and his successor, Guy Vernon Henry, on behalf of Puerto Rican autonomy. Muñoz Rivera and some friends would foil an assassination attempt by pro-American parties, meant to silence Muñoz Rivera's anti-American voice.
More threats to his life were made. Muñoz Rivera eventually moved to New York after leaving the newspaper El Diaro in the hands of one of his followers. He founded the Puerto Rican Herald, a bilingual newspaper in which he continued to advocate for Puerto Rican autonomy. Eventually helping to create the Union of Puerto Rico Party, in 1910, Muñoz Rivera was elected as the Resident Commissioner of Puerto Rico. President Woodrow Wilson made it clear that Puerto Rican independence would have to be dropped as the Union Party’s goal in order for the United States government to approve any amendments to the Foraker Act. Despite internal opposition within the Party, Muñoz Rivera was able to advance a policy to seek equality for Puerto Rico without statehood and autonomy without independence. When the Jones-Shafroth Act was passed, he was disappointed in the control over Puerto Rican government that was given to the United States Congress. He made a speech in which he declared that while Puerto Ricans would prefer American citizenship to any other, as long as Puerto Rico itself existed, they would want Puerto Rican citizenship. He died soon after due to cancer.
 Mack Reynolds, Puerto Rican Patriot: The Life of Luis Muñoz Rivera. New York: Crowell-Collier Press, 1969, p.64
 Puerto Rican Patriot: The Life of Luis Muñoz Rivera, p.76
 “Luis Muñoz Rivera”, Hispanic Americans in Congress, 1822-1995, Library of Congress, http://www.loc.gov/rr/hispanic/1898/munoz.html
 “Luis Muñoz Rivera”
 “Luis Muñoz Rivera”