The building that has survived to the present day is organized into three naves and features a Latin cross plan, the result of a long construction process. The main apse, built in the 16th century in the Hispano-Flemish style, replaced the original Romanesque one; however, the outline of this early apse can still be recognized today thanks to markings preserved in the floor of the main chapel, which were placed there following archaeological excavations. The side apses, on the other hand, do belong to the Romanesque period and are covered with barrel vaults, preserving the medieval character of the complex. Despite the expansions and renovations carried out during the time of Infanta Urraca and the architect Deustamben, the overall result is balanced and harmonious. These interventions were constrained by the earlier structure built by Ferdinand and Sancha, which is why the apses are not of equal width nor do they align exactly with the axis of the naves.

The central nave rises significantly above the side naves and is covered by a barrel vault, a solution also used in the straight section of the apse and in the transept, reinforcing the sense of verticality and monumentality of the space. The side naves, meanwhile, are covered with lower, more functional groined vaults. The arches separating the naves have a very pronounced camber, lending slenderness to the interior, while those of the transept are polylobed—a unique feature that reveals the survival of Mozarabic traditions and highlights the coexistence of different artistic influences in the church’s evolution.