The Diocese launched several programs and projects under the Pastoral Affairs Office. Most of the pro-poor services of the Laity are cascaded by the Pastoral Affairs Office through its seven Commissions: Worship/Liturgy; Education/Formation; Social Action; Stewardship; Family & Life; Temporalities and Youth. The services, programs, and projects are cascaded through the Council of the Laity of Novaliches (CLaN) to each Parish Pastoral Council (PPC) according to their needs and priorities.

Aside from the Pastoral Affairs Office or Department, the Diocese has an Administration Department, composed of the Chancery, Properties, Finance, and Tribunal Offices; which collectively handle the management of the Diocese.

Several Catholic schools run by Parishes have now been established under the management of the Roman Catholic Bishop of Novaliches Educational System (RCBN-ES) which is another Department of the Diocese.