The original floor plan could be reconstructed based on the archaeological excavations, consisting of a basilica floor plan with three naves and archways supported by columns, tripartite chevet with a straight back wall, and small access hall with vestibule, above which the royal tribune was constructed, where the king and his entourage would attend the liturgical services.

The sculptures carved in relief on the bases of the columns form an ensemble depicting the four Evangelists –Mark, Luke, John and Matthew–, seated under arches decorated with rope moulding. The evangelists are engaged in reading or writing, in scenes that evoke models from classical antiquity. Another example is the lattice on the southern wall, carved in a single piece, with triple camber archway, above which a there is a tympanum with interlocking circles that have been crafted with great expertise in the delicate latticework.

The reliefs on the jambs at both sides of the entrance to the temple are of great interest, not only due to the quality of the sculpture, but also because the motif depicted is not a religious subject, but instead pagan scenes alluding to circus games, an exceptional example in the European religious architecture in Europe, which has as its model the Roman-Byzantine consular diptychs, in specific of the consul Aerobindus (year 506).

The paintings form an unusually valuable grouping, since a human figure is depicted for the first time in Asturian art: a person seated on a throne and another image of a man strumming a musical instrument, probably a lute. The paintings reveal influence both from sculptural models from the High Middle Ages and from illuminated manuscripts.

The ensemble of wall paintings in the church was restored by the Spanish Institute for Cultural Heritage (Instituto de Patrimonio Cultural de España) between 2019 and 2020, and plant motifs and geometrical motifs have been recovered on the five vaulted ceilings: those of the central and side aisles, portico and tribune, as well as a Late Gothic religious scene in the apse, which features images of the coats-of-arms of the Solís and Álvarez families.

The Archaeological Museum of Asturias conserves an important collection of pieces originally from San Miguel de Lillo, including capitals, chancel screens, lattices, bases of columns and supporter of the altar; and the National Archaeological Museum conserves an ensemble of capitals, impost and components from the arches.

At the Church of San Miguel de Lillo/Liño services are held on specific occasions.