Lincoln was very clear–at least in public–that the Civil War was not fought over slavery: it was, he said, for the preservation of the Union first and foremost. So it's not surprising that when the conflict started he had no firm plan to emancipate the slaves in the borderland or Southern states. He also knew that such a move might prove very unpopular in the North.
So why did he issue the Emancipation Proclamation on January 1, 1863? There are many reasons. According to David Williams' fascinating new book I Freed Myself: African American Self-Emancipation in the Civil War Era (Cambridge University Press, 2014), an important and neglected one has to do with African American self-emancipation. After the war began, masses of slaves began to leave the South and head for the Northern lines. The Union forces received them as "contraband" seized from the enemy during wartime. As such, their status was uncertain. Many wanted to fight or at least serve as auxiliaries in the Union armies like freemen, but they were still seen as property. As Williams points out, the North certainly needed their manpower–as Lincoln knew better than anyone. Bearing this in mind, the President felt the time was propitious to do what he thought was right all along–free the slaves. Listen in.