The church is also denominated the Real Parroquia de los Santos Juanes (Royal Parish of the St Johns) or San Juan del Mercado (Sant Joan del Mercat in Valencian or St John of the Market) due to its location adjacent to the city Central Market and facing the Llotja de la Seda building.

A major fire in 1592 led to another reconstruction, commissioned by the Archbishop and Viceroy Juan de Ribera in an exuberant Baroque style completed in 1700.

This was located in the Boatella neighborhood, then working class quarters, outside the town walls, that housed some of the Morisco population.

The square exterior of the apse, facing the piazza, houses a central niche decorated with a stucco statuary group of the Virgen del Rosario (Virgin of the Rosary) attributed to Jacopo Bertesi.

The center is surmounted by a clock tower, and a roofline dominated by statues of the Juanes: including the Baptist, the Evangelist, and Saints Francesco Borgia and Luis Bertrán.