The first people known to have entered the area of Alachua County were Paleo-Indians, who left artifacts in the Santa Fe River basin before 8000 BC.

Artifacts from the Archaic period (8000 - 2000 BC) have been found at several sites in Alachua County.

[3] The Timucua-speaking Potano tribe lived in the Alachua culture area in the 16th century, when the Spanish entered Florida.

The Potano were incorporated by the colonists in the Spanish mission system, but new infectious diseases, rebellion, and raids by tribes backed by the English led to severe population declines.

[4] In the 17th century, Francisco Menéndez Márquez, Royal Treasurer for Spanish Florida, established the La Chua ranch on the northern side of what is now known as Payne's Prairie, on a bluff overlooking the Alachua Sink.

Lieutenant Diego Peña reported in 1716 that he passed by springs named Aquilachua, Usichua, Usiparachua, and Afanochua while traveling through what is now Suwannee County.

In the twentieth-century, anthropologist J. Clarence Simpson assumed the named springs were in fact sinkholes.

[6] The Spanish later called the interior of Florida west of the St. Johns River Tierras de la Chua, which became "Alachua Country" in English.

[7] Around 1740, a band of Oconee people led by Ahaya, who was called "Cowkeeper" by the English, settled on what is now Payne's Prairie.

In 1812, during the Patriot War of East Florida, an attempt by American adventurers to seize Spanish Florida, a force of more than 100 volunteers from Georgia led by Colonel Daniel Newnan encountered a band of Alachua Seminole led by King Payne near Newnans Lake.

[9][10] In 1814, a group of more than 100 American settlers moved to a point believed to be near the abandoned Payne's Town (near present-day Micanopy) and declared the establishment of the District of Elotchaway of the Republic of East Florida.

Wanton's Store, near the site of the abandoned King Payne's Town, attracted settlers, primarily from Europe, who founded Micanopy.

The 1823 Treaty of Moultrie Creek required the Seminole to move a reservation south of what is now Ocala, and the flow of settlers into the area increased.

In 1834, Hillsborough County was created, which included the area around Tampa Bay down to Charlotte Harbor.

[11] In 1853, the residents of Alachua County realized that the route of the planned Florida Railroad connecting Fernandina to Cedar Key would bypass Newnansville.

A general meeting at Boulware Springs was called to consider moving the county seat to a new town on the expected route of the railroad.

The motion to move the county seat was hotly contested by the residents of Newnansville, but Tillman Ingram, a plantation owner in Hogtown who owned a sawmill there, offered to build a courthouse in the new town.

[13] The first three documented lynchings, in Gainesville in 1891, involved two Black men and a White man, who were associated with the notorious Harmon Murray.

[17] The proposed amendment is the subject of a statewide, nonpartisan campaign [18] to place adoption of it before all Florida voters on the 2024 ballot.

Branch libraries opened in High Springs, Hawthorne, and Micanopy the next year, and a bookmobile was put into service.

A new, permanent location for the Cone Park Branch Library opened near the Eastside Community Center in Gainesville on December 14, 2013.

Prior to 2024, county commissioners were elected at-large, but a ballot measure passed in 2022 created single-member district seats.

In June 2007, ten employees in the sheriff's office, including the jail's director, were either fired or resigned while being investigated.

[43] As of 2015[update] the sheriff's office had at least one Lenco BearCat armored vehicle and two helicopters provided by the federal government under various programs.

[44] On August 9, 2021, a prison inmate, Erica Thompson, gave birth while being held in Alachua County Jail.