The Basilica del Pilar has several chapels of great artistic and historical value.

In the southeast corner, the first chapel on the right as you enter through the lower door was commissioned by Archbishop Tomás Crespo de Agüero and is notable for its late Bolognese Baroque style with allegorical frescoes and an altarpiece with the image of St. John the Baptist attributed to Gregorio de Mesa, as well as canvases by Pablo Félix Rabiella y Sánchez and possibly Jerónimo Lorieri; it also houses the popular 17th century Andalusian Baroque Cristo del Pilar (Christ of the Pilar).

The chapel of Santa Ana preserves a 19th century altarpiece with the image of Santa Ana with the Virgin and Baroque sculptures, together with Renaissance panels and a funerary monument to General Manuel de Ena. The chapel of San José has a 17th century baroque altarpiece with neoclassical additions and sculptures related to José Ramírez de Arellano, as well as canvases from the same century.

The Main Sacristy, closed to the public, keeps gold and silverware from the 15th century, tapestries, antique furniture, Renaissance and Baroque paintings, and other valuable objects. The chapel of San Antonio de Padua, built in 1713 and decorated in 1755, stands out for its marble and jasper altarpiece with polychrome sculptures and frescoes depicting the glorification of the saint. The chapel of San Braulio, in the neo-baroque style of the 19th century, contains the image of the saint along with pictorial and sculptural decoration.

The chapel of the Rosary houses a Herrerian altarpiece from circa 1601 with remarkable sculptures and Renaissance and Mannerist panels, as well as Baroque paintings. The chapel of San Agustín, also known as Parroquia del Pilar, preserves a late Baroque altarpiece with sculptures by Juan Ramírez de Mejandre and a lesser quality titular image. The chapel of San Pedro Arbués has a 19th century altarpiece with stucco relief and the processional image of the Christ of the Expiration. The chapel of San Lorenzo preserves baroque frescoes by Francisco del Plano and a neoclassical altar designed by Ventura Rodríguez with academic sculptures.

Finally, the chapel of San Joaquín has an 18th century gilded classicist altarpiece, an image of San Joaquín with the child Virgin and the tomb of the Duke of Montemar, hero of military campaigns in Italy. These chapels combine baroque, neoclassical and renaissance elements, and house important artistic works and liturgical functions within the basilica.