This diocese covers Sabah's interior districts of Keningau (including Sook), Nabawan (including Pensiangan and Sapulut), Sipitang, Beaufort (including Membakut), Tenom (including Kemabong), Tambunan and Kuala Penyu as well as a partial extraterritoriality jurisdiction on two districts in Sabah's West Coast Division, namely in the Bongawan area of Papar district, which borders the district of Beaufort via the township of Membakut and the Kiulu area of Tuaran district that are actually under the pastoral care of the Archdiocese of Kota Kinabalu; but has been allocated under the ecclesiastical purview of the Holy Cross Toboh and St Patrick's Membakut parishes of Beaufort as well as Tambunan districts within this diocese.

The first bishop is the Right Reverend Datuk Cornelius Piong, appointed on 17 Dec 1992.

There are 10 parishes and 1 mission located in the Diocese of Keningau (one outstation church in Tambunan district is under the pastoral care of St. Anthony's Church, Apin-Apin which is in turn, one of the sub-parishes of St. Francis Xavier's Cathedral, Keningau known as St. Paul the Apostle's Church, Kg.

Rantai, Apin-Apin Lama, Tambunan since it is located in the border of both districts along the Keningau-Tambunan highway (marks the parish borders between the cathderal and St. Theresa of Lisieux's Church in Tondulu, Tambunan) as well as extraterritorial oustation churches under Holy Cross Parish, Toboh, Tambunan located in a very remote area of the Kiulu sub-district of Tuaran in the northern part of Sabah's West Coast Division which partially surrounds Tambunan district (marks the diocesan borders between this church and St. Joseph Husband of Mary Parish, Kiulu/St.

John the Evangelist's Parish in Tuaran, which is under the care of Kota Kinabalu Archiocese), as well as St. Patrick of Ireland's Parish, Membakut, Beaufort located in the Bongawan area of Papar district in the southern part of Sabah's West Coast Division, along the border of the Papar as well as Beaufort districts, which also marks the boundary between the West Coast and Interior divisions of Sabah state (also marks the diocesan borders between this diocese and the Kota Kinabalu Archdiocese, between the borders of the parishes between this church and St. Joseph the Worker's Parish in Papar)).