On February 12, 1825, a group of Creek Indians, led by William McIntosh, signed the Treaty of Indian Springs in which they ceded all of their remaining lands in present-day Georgia.  Subsequently, in an act of June 9, 1825, the General Assembly provided that the land ceded by the treaty be divided into five sections, surveyed into districts and land lots, and distributed by land lottery (Ga. Laws 1825 Extra. Session., p. 3).  On December 14, 1826, the legislature redesignated the five land sections as the counties of Lee, Muscogee, Troup, Coweta, and Carroll and provided for the organization (Ga. Laws 1826, p. 57).

Despite the fact that the five counties were not named until December 14, 1826, the date their respective boundaries were established – June 9, 1825 – is generally accepted as the date of their creation.  Because the five counties were provided for in the same act, their order of creation is based on the order they were mentioned in the act – Lee, Muscogee, Troup, Coweta, and Carroll.  Thus, Lee was Georgia’s 61st county, while Muscogee was 62nd.

In 1971, work began on a new government building for the Consolidated Government of Columbus and Muscogee County. The new structure was built immediately behind the 1896 courthouse. After its completion, both old and new courthouses stood together briefly in 1972. Subsequently, the old courthouse was torn down.

The main community of Muscogee County is the county seat, Columbus.