The Église Saint-Bonaventure (French pronunciation: [eɡliz sɛ̃ bɔnavɑ̃tyʁ]) is one of the churches of the quarter Presqu'île, located on the Place des Cordeliers, in the 2nd arrondissement of Lyon.

To meet the needs of the community of Franciscan friars, named Cordeliers, installed at this place since the seneschal Grolée bequeathed them a space for the installation of their convent, the construction of a bigger church was decided by Jacques de Grolée, grandson of the seneschal, to overcome the narrowness of the first convent church, which was apparent when the crowd was gathered at ceremonies for the Cardinal Bonaventure's death, on the night of 14 and 15 July 1274, at the age of 57.

The church was consecrated on 18 September 1328 by the archbishop of Lyon, Pierre IV of Savoy, under the name of St. Francis of Assisi.

The restoration, handled by architect Renzo Wieder, focused on the main facade, stained glass windows, sculpted decor, and involved replacing metal clips and reconstructing sculptures as needed.

The Friday before Palm Sunday, the evening gathering is hosted by the inter-scout choir of Lyon which also gives its annual concert on 8 December.