The church that stands today features a Latin cross plan organized into three naves. The main apse, built in the Hispano-Flemish style and dating from the 16th century, replaced the original Romanesque apse, whose original layout can now be identified thanks to markings on the floor of the main chapel following archaeological excavations. The side apses, meanwhile, date from the Romanesque period and are covered with barrel vaults. Despite the expansions and renovations carried out during the reign of Infanta Urraca under the direction of the architect Deustamben, the complex presents a balanced and coherent appearance. These interventions had to adapt to the earlier church built by Ferdinand and Sancha, which explains why the apses do not exactly match the naves in width or alignment.

The central nave stands out for its considerable height and is covered by a barrel vault, as are the straight section of the apse and the transept, while the side naves feature groin vaults. The arches separating the naves have a pronounced camber, and those of the transept take on a poly-lobed shape, a feature that points to the survival of elements characteristic of Mozarabic art.