On his authority as President, Johnson attempted to get the seceded states back into the Union at once. His plan was modeled on Lincoln's procedure for dealing with conquered states during the war. However, the Radical Republicans, a faction favoring harsh treatment of the South, said that Congress, not the President, should determine when, and under what conditions, the Southern states were to be reestablished. A power struggle followed, with Congress upsetting Johnson's program by refusing to seat senators and representatives from Southern states that had formed new governments.

Congress then began enacting the program known as Reconstruction. The major aim was to require Southern states to grant blacks, freed from slavery by the 13th Amendment (1865), the right to vote. Black suffrage was necessary, it was argued, to protect the welfare of the blacks. Some Radicals also hoped to establish the Republican party in the South.

A Civil Rights Act, conferring full citizenship upon the former slaves, was passed in 1866. Congress then proposed the 14th Amendment, which gave the states a choice of enfranchising the blacks or having reduced representation in Congress. The amendment also barred Confederate supporters who had held state or federal office prior to the war from again holding office unless pardoned by Congress; more than 150,000 persons were affected by this provision.Tennessee promptly ratified this amendment and was readmitted to the Union in 1866. When the 10 other former Confederate states refused to ratify, Congress adopted stronger measures in 1867. These states were placed under military rule. The military commanders were authorized to arrange for and supervise conventions to establish new state governments with constitutions that conferred full citizenship on blacks. Blacks and loyal whites—that is, whites who professed loyalty to the Union—were to participate. After the legislatures of the new governments had ratified the 14th Amendment, the states could apply for representation in Congress.