In the nineties, numerous and important restorations were carried out in the building that transformed it in a noticeable way. On the one hand, the buildings that were attached to it were removed and, that way, sculptural elements that had been hidden were brought to light. Amazing mural paintings also appeared, as the fortified city that could be saved by tearing it from the wall, which can be today seen inside the nave. On the other hand, a complete restoration of the interior was carried out, bringing to light the original paintings. For this purpose, the baroque altarpiece was moved away and placed in a side chapel, and the medieval windows that had been covered could also be rescued. The old photographs allow us to see these important changes perfectly, as we can still see the school building that connected with the porch.

The possible promoters of this extension, the Otazu-Guevara family, built a funeral chapel for themselves on the north wall of the church. The entrance arch still has Gothic elements, while the paintings that cover the vaults are in Renaissance style. Until the recent renovations, the triptych of Saint Sebastian was in this chapel, a jewel of the mid-16th century that has few parallels in the province. In the centre, we see a sculpture of the Saint, while the four paintings of the doors describe the most important moments of his hagiography

A century later, in the 17th century, the sacristy was added, which today is covered by the apse in its northern area. Converted into a baptistery, it still preserves the magnificent vault made by Pedro de la Cuesta that connects perfectly with the Late Gothic chapel of the Otazu-Guevara family.

The main altarpiece, which is today in the aforementioned chapel, was in the east end of the church until a few decades ago. It is a simple work from the 17th century, formed by three horizontal and three vertical sections, whose gilding finished almost at the end of the 18th century. In the first panel, flanking the tabernacle, Saint John the Baptist and Saint John the Evangelist appear; in the second, the carving of the Virgin Mary is presented, titular figure of the temple, accompanied by Saint Joachim and Saint Joseph; finally, in the upper panel, we find the effigies of Saint Dominic and Saint Francis, with the scene of the Calvary in the central part.