Prior to the building of the church of Saint Ildefonso, a chapel, known as Santo Alifon, stood on the site. Its construction date is unknown, but several early texts mention its existence. The earliest known reference to the site and the original chapel is in a work by a bishop of Porto, Vicente Mendes, dated 1296.[1][2]

The aged chapel, in danger of collapsing, was demolished in 1709 and construction began on the new church that year. The building took thirty years to complete, finally inaugurated and blessed on 18 July 1739. The first stage of construction was completed in 1730, when the main body was finished and the tympanum, bearing the date M DCC XXX (1730), was placed. The second construction phase, from 1730 to 1739, saw the erection of the two bell towers, and the façade and narthex were finalised.[1][2]

The architect of the Igreja de Santo Ildefonso is unknown, although records exist giving the names of the carpenters, masons, and locksmith who worked on the building.[1][2]

Extensively repaired following a severe storm in 1819, the church also suffered damage from artillery fire on 21 July 1833 during the Siege of Porto. Over the years the church has undergone structural modifications and improvements, including the replacement of stained glass windows in 1967. The new ones were created by the artist Isolino Vaz.

During 1996 renovation works to the narthex, an area that corresponds to the original chapel's churchyard, nineteen graves were discovered.[1][2]