The interior of the Basilica del Pilar is organized in three naves, the central one being the widest, and seven sections supported by large pillars decorated with classicist pilasters. They are supported by entablatures that support domes on pendentives and vaults. In the lateral walls there are chapels covered with domes or vaults, and the interior decoration includes garlands and figures of putti, work of the sculptor Manuel Miguel Gálvez in 1871.

Following a clockwise route from the lower door, at the east end of the south façade, are the chapels of St. Anne and St. Joseph, followed by the main sacristy, and then the chapels of St. Anthony and St. Braulio until reaching the upper door. In the west section, next to the choir, there are four small chapels, among which the Ecce Homo and Buena Esperanza chapels stand out. In the area of the feet of the temple are the chapels of the Rosary and San Agustín, between which the chapter house is located.

On the north side, from the high door facing the Ebro, are the chapels of San Pedro Arbués, San Lorenzo, San Joaquín and the sacristy of the Virgin, leaving in the center the Pilarista Museum. In front of the Santa Capilla is the Coreto de la Virgen and, to the sides, the chapels of Santiago and San Juan, located next to the low door of the square, the main access for visitors.

The Pilarista Museum houses a collection of liturgical objects, crowns, jewelry and more than 350 mantles of the Virgin. Several archbishops of Zaragoza are buried in the temple, as well as St. Braulio and General Palafox.

An outstanding event occurred on August 3, 1936, when a Republican airplane dropped four bombs over Zaragoza. One fell in the streets of the city, another in the Plaza del Pilar, a third one perforated the roof of the temple and the last one hit near the mural of Goya in the Coreto. None of them exploded and two of them are kept as souvenirs in the basilica. Although many interpreted it as a miracle, later reports attributed the failure to technical defects, sabotage and the fact that the bombs were dropped at a very low altitude.

Finally, inside the basilica you can see the flags of Spain and Latin America, since the Virgin of Pilar is considered the patron saint of the Hispanic world.