The name of the church was always linked to the votive saint (San Giovanni Battista), however the remaining denomination has varied over the course of history depending on the owners. It was founded between the 11th and 12th centuries (the first historical signs date back to 1119) and belonged together with the hospital to the Knights Templar, from which the nickname of San Giovanni del Tempio derived; two centuries later the order was abolished and the property passed to the Knights of Jerusalem, who were later renamed Knights of Malta from which the current name of the church derives.
The popular name of the whole complex (which also includes the hospice of Santa Caterina) is San Giovanni dei Furlani; this nickname (also given to the nearby calle) originates from the fact that the area was once inhabited by a large group of families of Friulian origins.
The current appearance of the building is the result of the renovations carried out starting from 1565, which most likely involved the elimination of the wooden choir inside the church. The plan of the temple includes a single nave with a Gothic tympanum placed to crown the facade. Inside the presbytery the coats of arms of the knights and the prior in office of the order are depicted, while on the right wall you can see the "San Giovanni Nepomuceno" by Giambattista Piazzetta (1683-1754) and the "Baptism of Christ", work from the school of Giovanni Bellini (1430ca-1516), finally, inside the cloister, there are numerous tombstones belonging to the knights affiliated to the two orders who guarded the church.
The fall of the Republic entailed in the first place the expulsion of the Knights of Malta from the territory and secondly the stripping of most of the furnishings. Once the religious function was removed, the building first saw the birth of a printing house and later also a show room; when in 1839 the order of the knights returned to occupy the complex, the ancient function was restored and the furnishings were renewed by collecting various elements from other suppressed churches (altars, sculptures, paintings).