The church is structured differently from the previous pre-Romanesque buildings, since it features a cross-shaped floor plan with a single nave with vaulted ceiling adjoined by four rectangular spaces. It can be entered through a gate that communicates directly with a vestibule with vaulted roof, above which is the royal tribune, from which the king and his entourage attended the liturgical services.

It shares structural and decorative features with the building on Mount Naranco such as the barrel vault reinforced with transverse arches and the articulation of the walls with blind arcades. Noteworthy is the sculptural decoration in relief applied to the blind arcades of the walls, the capitals decorated with battling animals, bands and medallions, and the distinctive Asturian decoration with rope moulding.

The most striking portion of the temple is the triple arch and the chancel screens in front of the elevated altar, which separate the holy space reserved for clergy from that of the parishioners and which owes its existence to the celebration of the Hispanic liturgy.

The presbytery is structured with two blind arcades on the sides and a single rectangular apse (sanctuary), which is another original feature in pre-Romanesque art, where the triple chevet is more typical.

The hierarchical separation of the liturgical spaces in front of the sanctuary was added at a later date, in the 10th century, using pieces reused from the seventh century. The liturgical barrier is made up of a triple archway with arches resting on marble columns with capitals in the classical tradition. Set into the parts of the wall above the arches are five lattices with decorative motifs of Asturian and Mozarabic origin.

In the chancel or parapet that completes the lower part of the main arch, two panels of stone with beautiful carvings from the Visigothic era joined by a central small column have been reused, and they conserve an inscription that says:

“Abbot Flaino makes this offering in honour of the Apostles of the Lord, Sts. Peter and Paul)”.

This inscription and the fact that the pieces of the archways and chancels have been reused suggests the existence of la previous project.

The ornamentation of these components of the holiest liturgical space of the church refer to the Mystery of the Trinity represented in the sequences of three circles arranged in an ascending vertical position, which is reiterated in the three lattices embedded in the archway of the high altar. The iconography of Asturian pre-Romanesque art continually evokes the Adoptionist controversy regarding the three-person nature of the divinity.

The first mention of the Church of Santa Cristina de Lena is late, in the 17th century, and in the following century the church is mentioned by the painter Francisco Reiter and Gaspar Melchor de Jovellanos, who was the first to create a graphic representation of the church.

The current condition of the building is the result of various efforts of restoration over the last three centuries: the restoration of Juan Bautista Lázaro in 1893, based on the reconstruction of Jerónimo de La Granda; the rebuilding by Alejandro Ferrant in 1935, after the damage incurred during the revolutionary events of October 1934; the restoration of Luis Menéndez-Pidal y Álvarez between 1966 and1970, and the final effort in 2012, according to the master plan by Cosme Cuenca and Jorge Hevia.

At the Church of Santa Cristina de Lena, services are held on specific occasions.