Though archeological finds have pointed to traces of human activity as early as 100 BC, the earliest known full-time settlers to the islands were Anishinaabe peoples migrating from the east coast beginning around 950 AD, following the waterways comprising the established trade routes that had connected the eastern nations to western nations for thousands of years. Details and stories of these migrations were preserved in birch bark scrolls. The few of which that survived the eventual burning by the European missionaries, can now be seen being preserved in the Smithsonian Museum in Washington, D.C. As these migrations continued west, they created several prominent settlements, but when they discovered how to grow wild rice in the marshes of shallow Chequamegon Bay, they made Mooningwanekaaning (now Madeline Island) their capital, with settlements on Stockton Island and Manitou Island, as well as along the mainland shoreline.

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On and around these islands, the Ojibwa people discovered and innovated agricultural advancements, including excavating copper deposits and creating specialized tools for agriculture, hunting and fishing, the use of canoes for rice harvesting, conjugal collaborative farming, and the Three Sisters Crop Complex, enabling the Ojibwa to greatly expand their population, territory and power outward in all directions creating an enormous nation. However, these rapid advances in technology, along with five more centuries of migration from the east, also caused divisive ideological disagreements over traditionalism, and ultimately, the Potowatomi, Ottawa, and other tribes spliting off, leaving the Ojibwe alone wielding full control over the entire Lake Superior region, with the Islands remaining as their nations capitol.

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When the early French traders arrived around 1640, the capital city on Madeline Island was given the name La Pointe, and by 1693 it was fortified and included as an official Trading Post city in the Empire of New France, but with the westward expansion of European colonialism, conflicts boiled into formal wars from 1775 onward. Over the next 35 years, as more and more Native populations were concentrated into increasingly smaller areas, these areas became unable to provide sustenance for the swelling populations, and in 1811, the recognized principal, Chief Buffalo from La Pointe led an army of Ojibwa to fight in Tecumseh's War against the U.S.. However, he had a change of heart and pursued diplomacy when he met Michel Caddotte in Sault Ste Marie, who convinced him that by avoiding violence against the US, he could negotiate better treaties for the Ojibwa people. Though the American flag was hoisted over the Islands in 1816, Chief Buffalo fought decades with the United States government, and mining and lumber capitalist's continual and sometimes deadly efforts to completely remove the Ojibwe people, successfully securing permanent reserves of land including the mainland coastline nearest the Islands for the Red Cliff band, as well as entire reservations for other bands in the region.