The majority of the population is Roman Catholic, and in 2002, Quezon City was made an episcopal see for two new Catholic dioceses: Cubao and Novaliches, as the very populous Archdiocese of Manila was carved up and five new dioceses created. A number of religious orders have set up convents and seminaries in the city. Various Protestant faiths have seen a significant increase in membership over recent decades and are well represented in Quezon City.

While the Islamic faith has its largest concentrations in the south of the Philippines, there is a significant population in Quezon City. The Salam compound in Barangay Culiat houses one of the area's landmark mosques. The Members Church of God International popularly known to their television show Ang Dating Daan has many local chapters throughout the city and their extension in their administration office is also located here. The Iglesia ni Cristo (Church of Christ) Central Office is located in Quezon City.

The Church of Jesus Christ of Latter-day Saints has its Philippines Manila Temple located near the Libis area of the city while the Philippine Branch office of the Jehovah's Witnesses is located in San Francisco del Monte Avenue. The seat of the Presiding Bishop, the Cathedral of Sts. Mary and John of the Episcopal Church, the national offices of the United Church of Christ in the Philippines, the National Council of Churches in the Philippines as well as a number of Protestant seminaries are located in the city.