Mgr. Edmund Dunn succeeded Mgr. Jackson in 1900. Sandakan was by then an established mission with a presbytery, a boy's school and a convent. Limbahau also had a church, a presbytery, a school and a convent. Inobong, Penampang, Labuan, were all established missions. Jesselton (Kota Kinabalu) was opened in 1903. Beaufort, Kinuta, Tawau, Tuaran, Tambunan, and Tobo were started one after another.

Since the arrival of the Mill Hill Fathers, the Residence of the Prefect Apostolic was in Kuching. In February, 1927 Sarawak became a separate Prefecture under Mgr. Dunn. The Prefecture of North Borneo and Labuan, including Brunei, was placed under the care of Fr. A. Watcher who became Mgr. Watcher in July, 1927. Mgr. Watcher made Penampang his headquarters. From the year 1927 until the Japanese occupation in 1942, there was much progress. A junior seminary was established and a local sisterhood was started. The Carmelites arrived. Many schools were built and many outstations became headstations including Kudat, Tawau, Kuala Belait and Brunei town.

World War II halted all progress. During the Japanese Occupation all missionaries were interned except those holding German or Italian passports. Mgr. Watcher was still allowed to move around. The bombing of North Borneo started in March, 1945, the retreating Japanese rounded up the Prefect, seven Tyrolese Fathers and one Tyrolese Brother and took them to Tenom. They were never heard of again. The Fathers, Brothers and Sisters who returned to Sabah after their internment had to work under appalling conditions. Soon they build atap shacks as shelters. During the interim period the Prefecture was under Father Verhoven and later Father McCarthy as Prefect.

In 1946, Father James Buis was appointed Prefect Apostolic. In 1952, the Prefecture was raised to the dignity of a Vicariate to be known as the Vicariate Apostolic of Jesselton. Mgr. Buis was ordained Bishop and was made the first Vicar Apostolic of the new Vicariate. At the same time Brunei was detached from the Vicariate of Jesselton and placed under the jurisdiction of the Vicariate of Kuching. The Mission slowly recovered from the ravages of the war. The rebuilding of schools, churches and convents took place everywhere. The Pro-cathedral of the Sacred Heart was rebuilt in 1949. During the term of office of Bishop Buis the number of clergy, established parishes, religious congregations and schools reached an all time high. The clergy included the Mill Hill Fathers as well as a few Chinese Fathers from China whom Bishop Buis accepted into his Vicariate. Also some pre-war seminarians were by now ordained priests. The post war seminarians were also ordained. The first among them, Father Simon Fung, our late Bishop was ordained in 1963. The total number of clergy was 60. At the same time, places like Tanjong Aru, Beaufort, Telipok and Tandek all had resident priests. The number of Parishes with resident priests was 27. The Brothers of Christian Schools (La Salle Brothers) came in 1958 and the Daughters of St. Paul in 1960. The number of religious congregations thus reached 5. The schools were expanding and their number multiplying. There were altogether 53 primary schools and 25 secondary schools.