On September 22, 1862, Lincoln issued the preliminary Emancipation Proclamation, which announced that, in states still in rebellion on January 1, 1863, the slaves would be freed. He kept his word and, on January 1, 1863, issued the Emancipation Proclamation, freeing the slaves in 10 states not then under Union control, with exemptions specified for areas under such control. Lincoln's comment on signing the Proclamation was: "I never, in my life, felt more certain that I was doing right, than I do in signing this paper." He spent the next 100 days preparing the army and the nation for emancipation, while Democrats rallied their voters by warning of the threat that freed slaves posed to northern whites.

With the abolition of slavery in the rebel states now a military objective, Union armies advancing south liberated all three million slaves in the Confederacy. The Emancipation Proclamation having stated that freedmen would be "received into the armed service of the United States," enlisting these freedmen became official policy. By the spring of 1863, Lincoln was ready to recruit black troops in more than token numbers. In a letter to Tennessee military governor Andrew Johnson encouraging him to lead the way in raising black troops, Lincoln wrote, "The bare sight of 50,000 armed and drilled black soldiers on the banks of the Mississippi would end the rebellion at once". By the end of 1863, at Lincoln's direction, General Lorenzo Thomas had recruited 20 regiments of blacks from the Mississippi Valley.