In the mid-nineteenth century, Lewiston had an influx of Roman CatholicFrench Canadians that came to work in the local textile mills. Their arrival created the need for a French-speaking priest. Initially, masses in French were held in the basement of Saint Joseph's Church, until the number of parishioners attending the masses reached 1,000. Because of the large number of French-speaking parishioners, the masses were moved to the nave of Saint John's on July 2, 1870. By 1871, the number of parishioners had grown too large even for Saint John's. The following year, the cornerstone of Saint Peter's was laid, and the dedication mass was said in 1873. In 1881, the Dominican Fathers of Lille, France, and the Province of Québec took over the administration of the church. In 1899, the first reference to Saint Peter and Saint Paul was made, when the Dominicans published their Album Historique, calling the parishes S. Pierre S. Paul de Lewiston, Maine. In 1902, the parish was split to create the Saint Louis church, across the river, in Auburn.
By 1905, even after the split, the church had gained almost 10,000 parishioners. The old church had to be torn down, and the basement of the new church was finished in 1906. In 1907 and 1923, the Diocese of Portland requested that the parish be split, to create the parishes of Saint Mary's in 1907, and the Holy Cross and the Holy Family in 1923. Each time the parish divided, the money it had in its building fund to complete the church was also divided, delaying the top of the church from being built. Finally, in 1933, the Diocese of Portland allowed the parish to build the top part of the church. The church was finished on July 18, 1936, and was dedicated on October 23, 1938, to the saints the church bears the name of, Saint Peter and Saint Paul. On July 14, 1983, the church was added to the National Register of Historic Places, for being the second largest church in New England. In 1986, the Dominicans handed the administration of the church back to the Diocese of Portland. In 1991, the upper church started a renovation project that ended in 2002 with the dedication of a new altar. From 2002 to 2007, the chapel under the church was renovated and reopened, just in time for Mardi Gras, and—incidentally—Lent.