The apse is the most prominent section of the church, located between the Nativity and Passion facades. In its central cloister setting stands the chapel of the Assumption, flanked by two sacristies, one of which is already completed. Gaudí dedicated this apse to the Virgin Mary, whom he deeply admired. The design encompasses seven apsidal chapels, honoring the seven sorrows and joys of St. Joseph, in accordance with the wishes of Bocabella, the founder. The chapels are separated on the exterior by eight buttresses rising to 50 meters, with spires. Each chapel is highlighted by three stained glass windows at the top, framed by lower buttresses. Inspired by Gothic, its structure follows the layout of the crypt that lies beneath it. Construction took place between 1890 and 1893, although the vaults of the chapels and the ambulatory were completed in the early years of the 21st century.

The apse is embellished with a rich sculptural decoration, highlighting statues that pay homage to the founders of religious orders. Along the buttresses, from the Nativity to the Passion, are figures such as St. Clare, St. Bruno, St. Bernard of Clairvaux, St. Benedict of Nursia, St. Scholastica and St. Anthony Abbot. In the stained glass windows of the transept façade, St. Francis of Assisi and St. Teresa of Jesus appear, representing the Nativity and the Passion, respectively. The anagrams of Jesus, the Virgin and St. Joseph are also visible, each one impregnated with symbolism. The pinnacles of the buttresses culminate with sculptures of ears of corn and buds of native plants, previously part of the rural landscape, presented as a floral offering to the Virgin. In addition, at the top of the buttresses, there are gargoyles with animal shapes such as snakes, chameleons, snails, lizards, lizards, frogs and salamanders, creations of Llorenç Matamala. Inside the apse, 56 sculptures of angels on corbels, distributed among the seven chapels, are the work of Jaume Cases.

The raised railings of the apse chapels are decorated with floral motifs taken from the antiphon of the Little Office of the Blessed Virgin Mary, such as cedars, palms, cypresses, cinnamon trees, roses, olive trees and balsams. Also, the tops of the gables of the apse have a sculptural decoration that symbolizes the fruits of the Virgin Mary, such as rose hips, cinnamon, dates, olives and grapes. The lanterns of the chapels display the symbols of the antiphons corresponding to the last week of Advent, known as the "O antiphons".