When the federal government approved creating black units, Garnet helped with recruiting United States Colored Troops. He moved with his family to Washington, DC, so that he could support the black soldiers and the war effort. He preached to many of them while serving as pastor of the prominent Liberty (Fifteenth) Street Presbyterian Church from 1864 until 1866. During this time, Garnet was the first black minister to preach to the US House of Representatives, addressing them on 12 February 1865 about the end of slavery, on occasion of the passage of the Thirteenth Amendment.