Lee, who had opposed secession and remained mostly indifferent to politics before the Civil War, supported President
Andrew Johnson's plan of Presidential
Reconstruction that took effect in 1865-66. However, he opposed the Radical Republican program that took effect in 1867. In February 1866, he was called to testify before the Joint Congressional Committee on Reconstruction in Washington, where he expressed support for President
Andrew Johnson's plans for quick restoration of the former Confederate states, and argued that restoration should return, as far as possible, the status quo ante in the Southern states' governments (with the exception of slavery). Lee said, "every one with whom I associate expresses kind feelings towards the freedmen. They wish to see them get on in the world, and particularly to take up some occupation for a living, and to turn their hands to some work." Lee also expressed his "willingness that blacks should be educated, and ... that it would be better for the blacks and for the whites." At a time in early 1866 when most northerners opposed black suffrage, Lee warned that granting suffrage would be unpopular. "My own opinion is that, at this time, they [black Southerners] cannot vote intelligently, and that giving them the [vote] would lead to a great deal of demagogism, and lead to embarrassments in various ways."
In an interview in May, 1866, Lee said, "The Radical party are likely to do a great deal of harm, for we wish now for good feeling to grow up between North and South, and the President, Mr. Johnson, has been doing much to strengthen the feeling in favor of the Union among us. The relations between the Negroes and the whites were friendly formerly, and would remain so if legislation be not passed in favor of the blacks, in a way that will only do them harm."
In 1868, Lee's ally
Alexander H. H. Stuart drafted a public letter of endorsement for the
Democratic Party's presidential campaign, in which
Horatio Seymour ran against Lee's old foe Republican
Ulysses S. Grant. Lee signed it along with thirty-one other ex-Confederates. The Democratic campaign, eager to publicize the endorsement, published the statement widely in newspapers. Their letter claimed paternalistic concern for the welfare of freed Southern blacks, stating that "The idea that the Southern people are hostile to the negroes and would oppress them, if it were in their power to do so, is entirely unfounded. They have grown up in our midst, and we have been accustomed from childhood to look upon them with kindness." However, it also called for the restoration of white political rule, arguing that "It is true that the people of the South, in common with a large majority of the people of the North and West, are, for obvious reasons, inflexibly opposed to any system of laws that would place the political power of the country in the hands of the negro race. But this opposition springs from no feeling of enmity, but from a deep-seated conviction that, at present, the negroes have neither the intelligence nor the other qualifications which are necessary to make them safe depositories of political power."
In his public statements and private correspondence, however, Lee argued that a tone of reconciliation and patience would further the interests of white Southerners better than hotheaded antagonism to federal authority or the use of violence. He repeatedly expelled white students from Washington College for violent attacks on local black men, and publicly urged obedience to the authorities and respect for law and order. In 1869-70 he was a leader in successful efforts to establish state-funded schools for blacks. He privately chastised fellow ex-Confederates such as
Jefferson Davis and
Jubal Early for their frequent, angry responses to perceived Northern insults, writing in private to them as he had written to a magazine editor in 1865, that "It should be the object of all to avoid controversy, to allay passion, give full scope to reason and to every kindly feeling. By doing this and encouraging our citizens to engage in the duties of life with all their heart and mind, with a determination not to be turned aside by thoughts of the past and fears of the future, our country will not only be restored in material prosperity, but will be advanced in science, in virtue and in religion."
Lee applied for, but was never granted, the postwar
amnesty offered to former Confederates who swore to renew their allegiance to the United States. After he filled out the application form, it was delivered to the desk of Secretary of State
William H. Seward, who, assuming that the matter had been dealt with by someone else and that this was just a personal copy, filed it away until it was found decades later in his desk drawer. Lee took the lack of response to mean that the government wished to retain the right to prosecute him in the future.
Lee's example of applying for amnesty encouraged many other former members of the Confederacy's armed forces to accept restored U.S. citizenship. In 1975, Lee's full rights of citizenship were posthumously restored by a joint
U.S. Congressional resolution effective
June 13, 1975. At the
5 August 1975, signing ceremony of the
pardon, President
Gerald R. Ford acknowledged the discovery of Lee's oath of allegiance by Elmer Oris Parker, an employee of the
National Archives in 1970.