Despite Kentucky's allegiance to the Union, few Kentuckians supported Lincoln or the Republican administration. From the beginning of the war, many in the state worried that Lincoln meant to abolish slavery. Throughout 1861, Lincoln assured the state that he had no intention of interfering with the state's "domestic institutions." However, by the spring of 1862, he realized that the war would result in the demise of slavery. In March of that year, Lincoln offered to compensate slaveholders in the Border States if they accepted a plan of gradual emancipation. When the congressional delegations for those states turned down his offer, he realized the need for presidential action and in September issued the preliminary Emancipation Proclamation. Following this edict and the final version, which Lincoln signed on January 1, 1863, Kentuckians protested all efforts to abolish slavery. In 1865, the Kentucky General Assembly rejected the Thirteenth Amendment, which the state did not officially adopt until 1976.

Although Kentuckians opposed federal emancipation policy, their dissatisfaction intensified once the federal army began enlisting black soldiers. In the summer of 1863, General Jeremiah T. Boyle, commander of the Department of Kentucky, warned that enlisting blacks into the military would "revolutionize the state." Realizing the delicate situation in Kentucky, Lincoln initially exempted the state from black enlistment. However, by March 1864, recruiting stations had opened across the state and male slaves and free blacks flocked to join the army. White Kentuckians did all they could to curb black enlistment, even resorting to violence on occasion. Prominent politicians and other public figures harshly criticized the Lincoln administration. Colonel Frank T. Wolford and Lieutenant Governor Richard T. Jacob used such vitriolic rhetoric that military officials in Kentucky arrested them (Lincoln ordered that both be released). Until the end of the war, Kentuckians resisted federal emancipation policy, and after December 1865, when the Thirteenth Amendment abolished slavery, they expressed their disillusion by politically siding with the former Confederacy throughout the postbellum era.