According to the United States Census Bureau, the Middleburg CDP has a total area of 19.6 square miles (50.7 km2), all land.

Fort Heileman, a wooden stockade fortification located between the North and South prongs of Black Creek, was hastily built in 1836 and protected settlers at Garey's Ferry where it was the "principal depot for the east coast of Florida.

Garey's Ferry expanded following the Seminole Wars, growing quickly and trading in timber, citrus fruits, cotton, and farm crops.

On October 23, 1864, during the American Civil War, the 4th Massachusetts Volunteer Cavalry engaged local Confederates in a skirmish from their base at the Magnolia Springs hotel.

The 2nd Florida Cavalry, under command of Captain J.J. Dickison, retaliated by firing on the Massachusetts regiment, leading the latter to retreat across Black Creek and burn the ferry bridge behind them.

[16] The exact location of Halsey's Plantation is not known, but it was near the site that is currently Shadowlawn Elementary School on County Road 218.

"[20] According to "Embedded in Clay,"[clarification needed] Forman fled to South Carolina after his house was burned by a white mob.

Since the 1990s, Middleburg's population and industry have rapidly expanded along with the surrounding communities of Orange Park, Lakeside, Lake Asbury, Fleming Island, and Jacksonville.

Because of this development, construction to extend the First Coast Expressway through the area is underway, including the addition of exit junctions in Middleburg, Green Cove Springs, and Asbury Lake.