García Moreno's conservative reign arguably gave the Roman Catholic Church more power in Ecuador during the nineteenth century than it had in any other country in the world. This would all change with the rise of Eloy Alfaro and Radical Liberal Party. Alfaro was the antithesis of Moreno, and their differences were further accentuated by their historical juxtaposition.

The Roman Catholic Church and its conservative allies did not give up their power gracefully. Ecuador suffered a bloody civil war in which Catholic Church regularly urged its faithful masses to rise in rebellion against the Liberals. Oddly, a prolonged war was avoided largely because of the efforts of Catholic Archbishop Federico González Suárez, who urged the Church stay out of politics.

Religious paintingsadorned all public buildings during Moreno's rule, but were largely replaced with secular art after Alfaro took power.

Ecuador's political situation remained tumultuous even after the defeat of the conservatives, as a result of political infighting within the PLR. Most remember Alfaro as the central figure in the Liberal Revolution, though, in reality, he grudgingly shared control of the PLR with General Leónidas Plaza Gutiérrez and the two vied for the party's leadership until Alfaro's death at the hands of a Plaza-instigated mob.

After Alfaro's murder, Plaza served a second presidential term, however, by this point the coastal agricultural and banking interests, popularly known as la Argolla ("the Ring"), controlled the PLR more than Plaza did. And though la Argolla publicly advocated the Liberal cause, in practice it did little more than use the PLR and the Government to line its own pockets. La Argolla's abuse of power combined with the decline in world demand for Ecuadorian products pitched the country into a severe economic depression. Ecuador's worsening economic situation and the popular unrest it manifested set the stage for a bloodless coup d'état in July 1925 that officially marked the end of Liberal rule.

Church turned factory during the transition from Conservatism to Liberalism.

After the Liberal Revolution and thirty years of Liberal rule, the Catholic Church lost much of its hold on Ecuador. For example, Roman Catholicism was no longer the constitutionally mandated state religion, education was secularized, and civil marriage and divorce were legalized. In addition to tethering the Catholic Church, the era of Liberal rule sparked the development of Ecuador's infrastructure and economy. Alfaro and subsequent Liberal Administrations completed a number of important public projects such as the Quito-Guayaquil Railway.