The first known European to settle on Manitoulin Island was a French Jesuit named Father Joseph Poncet. Poncet established a Jesuit mission near Wikwemikong in 1648. The Europeans brought with them diseases that spread throughout the island. In an effort to cleanse the Island of these diseases, the Five Nations Iroquois conducted raids to drive out the Jesuits. It is said that the Iroquois burned the island before they left in an attempt to purify it.
Manitoulin would remain largely vacant until after the War of 1812 when the Odawa, Ojibwe and Potawatomi tribes began returning to the island. In 1836 the island was ceded (handed over) to the Crown to be used as a refuge for natives who were loyal to the British. The treaty of 1836 resulted in more native people seeking refuge on the island.
In 1838, Jean-Baptiste Proulx took up residence on the island at the request of the people of Wikwemiong. He re-established a Roman Catholic mission on the island. By 1842 Wikwemikong had 78 buildings for 94 famillies.
The Jesuits took over the mission in 1845. As part of the Jesuits takeover of the mission, they continued to develop the area by building a school, teacher's residence, training centre for agriculture and trades, sawmill and grist mill.
In 1848 the Jesuit priests and parishoners began planning for a permanent church structure. Father Nicholas Point, was an experienced architect and artist and is credited with the design of the Holy Cross Church. Construction on the church began in June 1849. The church was constructed out of limestone blocks, many of which had to be brought over from surrounding island. It was built by local people under the supervision of the priests and brothers. The cornerstone was laid on the day of the feast of St Ignatius (July 31, 1849).
The church officially opened for mass in July 25, 1852. In 1899 a steeple was added to the church.
Both the church interior and adjacent residence were destroyed by a fire in 1954.
By the mid 19th century (1862), the government was under pressure to open up more land to European settlers. The native people of Manitoulin were offered a treaty that would give the head of each family 100 acres of land located on a settlement. In return the natives would cede the land over to the government.
Tribes from the western parts of the Island agreed to the treaty. The Wikwemikong chief refused to accept the treaty and to this day Wiki remains unceded.
The remains of the church can be found on Wikwemikong Way in Wikwemikong. The Debajehmujig Theatre Group performs on the church grounds during the summers.