The Lafontaine area was settled in the early 19th century by four waves of French-speaking immigrants The first, French-Canadian and Métis settlers, were former voyageurs – fur traders who traveled from Montreal to the interior to trade with the native peoples – and their families, who had settled on Drummond Island and been forced to leave when it passed into American possession after the War of 1812.

The Reverend Amable Charest provided the impetus for the arrival of the next group of settlers. Father Charest was a missionary in Penetanguishene, and a native of Sainte-Anne-de-la-Pérade, near Trois-Rivières, Quebec. Recognizing the agricultural potential of the region, he encouraged families from his native province to settle in the new concessions.

This first wave of Québecois families arrived in 1841 from Batiscan. They were followed by a group of families from Joliette and, later, a group from Vaudreuil-Soulanges.
With no church in the area, people had to travel to Penetanguishene, 15 kilometres away, for mass. In 1850, to meet the spiritual needs of the newcomers, Father Charest began celebrating Mass in a private house in the 16th concession and founded the mission of Sainte-Croix that same year.
The first chapel of Sainte-Croix, built in 1856, was a log structure located immediately in front of the present church. The first permanent for the mission was Reverend Étienne Gibra, who arrived from Quebec in 1861.
Father Gibra enlarged the log chapel and added a sacristy. In 1870, he also oversaw the construction of a second log chapel, 10 kilometres to the south, to serve the Irish Catholic immigrants who had settled around what is now Perkinsfield.
Construction of the present church and rectory began in 1873, under the pastorship of the Reverend Joseph Michel. Lafontaine was not a wealthy community and Father Michel, who had received a substantial inheritance from his family, paid most of the cost from his own pocket.

All materials used in the construction of the new church were local – fieldstones cleared from farms made the foundation, local trees were felled and turned into boards in nearby sawmills, the bricks were made ofclay dug nearby and formed and fired by a parishioner, Louis Thanasse,
and the interior columns and arches were hand-carved by local woodworkers.

The new church, completed in 1877, was situated behind the old one. During the years of construction, the earlier log church continued in use for services and was then demolished.
In 1884, Father Michel extended his generosity to the Perkinsfield community, personally paying for the construction of a new church, St. Patrick’s, to replace Father Gibra’s log chapel there. The following year, he also arranged and paid for the building of a convent and school for girls in Lafontaine, beside the church of Sainte-Croix.

In 2000, Sainte-Croix commemorated the historic French Catholic presence in Ontario with the installation a stained-glass triptych representing the 1615 mass, celebrated by the pioneer missionary Father Joseph Le Caron, before Samuel de Champlain, at the Huron village of Carhagouha, four kilometres to the northwest of this site.