Catholic mission in Maumere began when Dominican Fathers Joao Bautista da Fortalezza and Simao da Madre de Deus arrived in Paga and Sikka, respectively, in 1566. Both missioners spread Catholicism along the Flores coast. As a result, Maumere had 200 Catholic families in 1613.
In 1862, Father J. Fransen from Larantuka visited Catholics in Maumere and asked them to build a new mission station. Jesuit Father Metz came in 1863 and worked together with Father Fransen to develop the mission. Two other Jesuits, Fathers Dijkman and Omzigt, followed Father Metz in 1864 and worked in Maumere. By then, local Catholics numbered 6,310.
In 1873, Father Omzigt, the mission superior, established St Joseph Church, which today serves as the diocesan cathedral. Afterward, several more Jesuit priests and brothers as well as Sisters of Charity came. They built new mission stations, schools and student dormitories.
The apostolic prefecture of Lesser Sundas (Nusa Tenggara), which also included Flores, was erected in November 1913. Divine Word Bishop Petrus Noyen was appointed apostolic prefect, and Divine Word priests took over mission work from the Jesuits. Similarly, the Missionary Sisters, Servants of the Holy Spirit took over the work of the Charity sisters.
By 1914, the Catholic population had grown to 17, 402.
On Dec. 12, 2005, the Vatican announced the establishment of Maumere diocese. Based in Maumere town, it covers Sikka district. It had been one of Ende archdiocese's three vicariates. The other two are Ende, which covers Ende district, and Bajawa, which covers Ngada district.
On April 23, 2006, Monsignor Vincentius Sensi Potokota was ordained the new diocese's first bishop. He was appointed archbishop of Ende on April 14, 2007, after the sudden death of Archbishop Longinus Da Cunha.
Maumere diocese covers an area of 1,731,932 square kilometers. It borders Larantuka diocese in the east and Ende archdiocese in the west.