The Soldier’s home was also important in the boldest action that Lincoln would take during the Civil War, the Emancipation Proclamation. Although Lincoln believed in ending slavery, the tenuous hold the Union had on loyal slave-owning border states, and his wish to create a larger consensus in Congress inhibited him from issuing a sweeping order to free the slaves. But as the war dragged on, Lincoln realized that he could no longer wait. During the summer of 1862, in the peace and quiet of the Soldier's Home, Lincoln began to draft the Emancipation Proclamation, and on January 1, 1863 issued the statement that gave thousands their freedom.

During the family's stay at the home, Lincoln would rise before 6:00am and make his daily trip to the White House. He always rebelled against large security escorts, but by 1862, the Secretary of War, Edwin M. Stanton, convinced Lincoln to accept a security detail of  25- 30 cavalry for his daily commute. Even though Lincoln was the victim of a failed assassination attempt in 1864, he would complain "it would never do for a president to have guards with drawn sabers at his door, as if he fancied he were, or were trying to be, or were assuming to be, an emperor."