In the struggle for unification of the country, between 1291 and 1304, Wiślica was ruled by Czechs. The supporting Bishop of Cracow, Jan Muskat, destroyed two churches in the city and erected a defensive tower. Despite that, Władysław the Short found support in Wiślica. The remains of the second collegiate date from this period, well preserved in the basement of the present Church, which is the third collegiate.

In its interior, the underground of Basilica hide the remains of two Roman churches..
The Church, which in 2004 upon award by John Paul II received the honorary title of minor basilica, was funded by king Casimir the Great.