It has a single-nave floor plan with chapels set between the buttresses, not connected to one another. The vault of the central nave is a barrel vault, resting on transverse arches which in turn rest on beautiful pilasters. The main chapel is preceded by a large arch bearing the coat of arms of Bishop Don Antonio Brizuela y Salamanca. The presbytery is covered by an interesting pseudo-oval dome on pendentives, built in the 17th century. At the foot of the church stands the raised choir, supported by two columns, and the bell tower. The original main altarpiece, of which only the attic section survives intact, is a Baroque work, also completed in the second half of the 17th century, though gilded in 1737 by the master craftsmen Manuel Pancorbo and Antonio Clavijo. It shows a three-section structure divided by Solomonic columns, with an attic section housing an image of Christ Crucified. This church has seven side chapels, traditionally linked to particular families. During the Civil War, the original altarpieces disappeared, along with the rich collection of religious imagery from its altars. • Chapel of San José • Chapel of Nuestra Señora de los Dolores • Chapel of San Antonio • Chapel of María Auxiliadora • Chapel of the Souls (Ánimas) • Chapel of the Veracruz • Chapel of the Señor de la Columna

The popular veneration of the titular Christ is linked to a deadly plague epidemic that devastated the town in 1833, which subsided after residents agreed to carry the image of the Crucified Christ in procession, after which the epidemic receded and the sick recovered. In thanksgiving, the hermitage was remodelled, its features of interest being the ashlar semicircular-arched doorway and the single-tier bell gable, and the dedication of its titular image was changed.

Around the 18th century, the hermitage of the Virgen de Atocha was built over the remains of a cemetery. We do not know exactly the date or year of her apparition, but it is linked to the apparition of the Virgen de Atocha of Madrid, as both refer to the same Virgin. The story goes back a long way, as oral tradition holds that one day the great Lady appeared where her hermitage now stands. Seeing that it was the same Virgen de Atocha venerated in Madrid, people decided to return her to the Spanish capital. She appeared again at the same spot, and once again they took her to Madrid, and so on, until they decided to leave her here, as she seemed unwilling to leave Villardompardo — and so it was, once her hermitage was built. Over the years, all the people of Villardompardo came to worship her and hold great faith in her.

On either side, two flared circular windows with polylobed outlines embellish the façade, which ends in a continuous moulding leading to the eaves. At the foot of the church, a prominent vertical section rises, topped by a bell gable that stands taller than the rest of the church, divided into two levels for bells: the first with two semicircular-arched openings, and the second with a single opening crowned by a small pediment bearing a cross at its apex. Below, a small door with large voussoirs, aligned with a raised semicircular-arched window above, gives verticality and marks the symmetry of this section. It stands on a small, charming square, the Plaza de la Constitución, raised above its surroundings and bordered externally by a platform with stone pillars topped with balls and linked by a wrought-iron railing. On one corner outside stands a charming stone fountain bearing the emblem of the Order of Calatrava, crowned with broken and mixtilinear mouldings in the Baroque taste.

Its floor plan features three naves, with the central one wider than the rest. The pillars separating the naves have different layouts, and the arches connecting the central nave with the side naves are semicircular, except in the Gothic area of the presbytery, where they are naturally pointed. A barrel vault covers the three bays of the central nave, which is lined by a cornice and defined by false transverse arches resting on buttresses. The presbytery, built in the 14th century, is constructed of ashlar and roughly hewn stone, though only partially, and is covered by a rib vault with tiercerons, diagonals and a ridge rib. The passage from the nave into the presbytery is emphasised by a large pointed chancel arch with roll mouldings and Gothic capitals decorated with lilies. In contrast due to their more recent date are the sacristy, located at the start of the left-hand side, balanced on the opposite side by a chapel. At the foot of the church stands the choir, raised on Solomonic columns, with a wooden balustrade and three basket-handle arches.

It has a single rectangular nave in the shape of a Latin cross, flanked by side chapels and presided over by an apse-less presbytery. The church is covered by a Mudéjar coffered ceiling with a simple tie-and-collar-beam structure, with five ornamented tie beams decorated with strapwork resting on corbels, which, beneath the choir loft, rest on a transverse beam supported by an Ionic column and a wooden bracket decorated with large acanthus leaves. In this same spirit of austerity, the side doorway was built a century later: a lintelled opening with Tuscan pilasters and no decorative elements. During the Civil War, the wooden altarpiece presiding over the Señor de las Aguas was destroyed, and in 1949 another was installed in its place, presiding over the Señor de la Capilla, a name by which this church is also known. The current bell tower, which replaced a bell gable that collapsed in the early 20th century, was built in 1956–57 on a square, prism-shaped base, with a first section featuring vertically arranged oculi on its shaft, framed by a shared moulding; the second section, smaller and octagonal, has pinnacles at its corners and pairs of semicircular arches for the bells, and is topped by a pyramidal spire.