The main altarpiece of Baroque style and the organ were built in the seventeenth century. The latter was enlarged in the eighteenth century. In the nineteenth century, the main nave was demolished given its poor condition and a new nave was erected along with an apse, but the two eighteenth-century chapels were preserved. During this period, the main facade with its characteristic bell towers was also remodelled. The new nave was moved from its original location, which made possible the creation of an atrium that would move the church gate away from the main irrigation canal, as the flood of the canal caused continuous flooding in the temple. In 1909, Luisa Antoine Larrea, who belonged to one of the most famous families in town, the Prytz family, donated the stony and grille fence that for many years confined the entrance atrium. The facade of the church has become one of the emblematic icons of Sant Joan d’Alacant.

In 1936, at the beginning of the Spanish Civil War, the church was assaulted and the altarpieces, the bells, the images and the objects of cult were destroyed. Among the main losses we can highlight the image of the Holy Christ of Peace, the Baroque organ, the altarpiece of Our Lady of the Rosary (of Churrigueresque style), and the ark where, according to tradition, the Holy Face was kept on its arrival in Sant Joan in the fifteenth century.

After the war the church was rebuilt. At present, some interesting pieces have been preserved such as the altarpiece of the Holy Christ dated from the eighteenth century, the safe-keeping room with frescoes by Heliodoro Guillén, the altarpiece of the Holy Face (eighteenth century), the canvas of the Holy Family by Antonio Villanueva (eighteenth century), and several sacred ornaments among which a silver gilded pyx dated from the seventeenth century stands out.

The facades and central nave were restored in the 80s thanks to the impulse of the parish priest Carmelo Dávila. The chapels were restored in the late 90s, and the atrium was renovated by eliminating the gate that the Prytz Larrea family had donated. In a corner, a small portion of that fence has been left as testimony to the era.

The Parochial Church of San Juan Bautista is one of the most important patrimonial elements of Sant Joan d’Alacant, a place intimately linked to the collective memory of its citizens and a reference for those who love the municipality.