The famous Quaker naturalist William Bartram passed through this area of Florida in 1774. He was looking at the flora, the fauna, the landscape and enjoying peaceful interactions with the Seminoles who lived in the area. He spent some time near what is now Micanopy with Seminole Chief Cow Keeper in the settlement at Cuscawilla. Bartram collected botanical specimens and later published a book named "Travels..." that Coleridge, Wordsworth and Emerson all said was an inspiration for their works.

Wanton's town was founded on this spot in 1821 as the first non-native settlement in inland Florida. The settlement was a mix of incoming American settlers and Seminole Indians (this was in the years between the First and Second Seminole Wars). Spain had transferred the title to Florida to the United States in 1819 but it was 1821 before American troops started to arrive, 1825 before any semblance of government came into being. It was in 1825 that Wanton's town was formalized as the town of Micanopy (named for another Seminole chief).

In those days, Micanopy was being developed by the Florida Association of New York (Florida's first development corporation and operated from New York City).

Micanopy was the center of civilization in this part of Florida until the railroads came. During the Second Seminole War both Fort Defiance and Fort Micanopy were built here. Some of the bloodiest battles of that war were fought along the road between Fort Micanopy and Fort Wacahoota (to the southwest but still within Alachua County).

The Florida Railroad planned to build across Florida from east to west - Fernandina to Cedar Key, however, the route chosen across Alachua County ran to the north of Payne's Prairie (just north of Micanopy) and that caused most businesses in the area to move to what is now Gainesville by 1859 (when the railroad arrived in actuality).

Today, Micanopy is a place where time seems to have stood still, where Old Florida still lives. Big, Spanish moss-draped live oaks, old Southern mansions, a very laid-back way of life. The historic district was listed on the National Register of Historic Places in 1983. South of town is the Tuscawilla Preserve, a 518-acre property permanently preserved by the Alachua Conservation Trust for the use of the local flora and fauna. Just across the road from that is the Micanopy Native American Heritage Park, site of an ancient burial mound from the days of the Mississippian culture when this area was occupied by the Timucua people. North of town is the vast Payne's Prairie State Preserve, a wonderland of Florida flora and fauna.

The major motion pictures Cross Creek (1983) and Doc Hollywood (with Michael J. Fox in 1991) were filmed in and around Micanopy. Conservationist Marjorie Harris Carr and her famous zoologist, conservationist, author husband Dr. Archie Carr lived for many years just outside Micanopy near Wewa Pond.

The population of Micanopy is down about 8% since 2000.