The Omena settlement had its beginnings when Aghosa Indians started arriving in 1850. In 1852, the Reverend Peter Dougherty and a band of Ottawas and Chippewas led by Chief Ahgosa moved from the present-day Old Mission Peninsula to a beautiful little bay on the Leelanau Peninsula's eastern side. Chief Shabwasung and his Ottawa band were already encamped on the point to the north of the bay, on land Chief Ahgosa and his families from Old Mission had purchased. Ahgosa settled a little to the north, and his village became Ahgosatown. Both bands became part of the New Mission, soon to be called Omena. Young George A. Craker came with Dougherty and taught farming to students in the mission school, and he and his descendants became active workers in Dougherty's Grove Hill New Mission Church. Now called the Omena Presbyterian Church, it was dedicated in 1858 and has stood as the oldest Protestant Church in Leelanau County and one of the oldest historical landmarks in Northern Michigan. The Ahgosa family was also very active and some are now buried in the mission cemetery.
In 1868 the mission farm was sold to Valentine Miller, who put out a dock. Miller's dock made it possible for summer tourists to disembark, when passenger ships arrived in the area. In 1884 a group of Cincinnati businessmen purchased the mission school, and it was remodeled to become the Leelanau Hotel. Within 35 years Omena blossomed into a tourist haven, with the Omena Inn, the Shabwasung, the Clovers, and Sunset Lodge, together with many resort cottages on Omena Point. When the railroad came through in 1903, Omena had two stops, one being at the Clovers resort. The A. F. Anderson Store benefited by all of this activity and operated in Omena for 47 years, beginning 1883. Since 1976 this landmark has been the location of Tamarack Craftsmen Gallery. Nearby, Paul Barth's general store, established 1889, remains as the Omena Bay Country Store. The early discovery of Leelanau County as a resort haven helped to sustain pioneer families by providing commerce and income, just as it does today.