The main difference between presidential Reconstruction and Congressional Reconstruction was that presidential Reconstruction was much more lenient toward the South. Because the “Radical Republicans” in Congress did not like this, they overrode President Johnson’s wishes and implemented a harsher variety of Reconstruction.
Before he died, President Lincoln had been eager to bring the states that had seceded back into the Union. He felt that it was important to heal the wounds from the war and wanted to be easy on the South. Therefore, he proposed a plan that allowed the states to reenter the Union as long as 10% of the people who had voted in the 1860 election swore an oath of allegiance to the US. After Lincoln died, President Andrew Johnson implemented a very similar plan.
However, the Radical Republicans were not satisfied. They were particularly angry because the South instituted the “black codes” that treated the freed slaves harshly. The Radical Republicans felt that the South had not learned its lesson from the war and that the South was trying to reinstitute slavery in a de facto way.
Therefore, Congressional Reconstruction was implemented. It was much harsher than presidential Reconstruction. It instituted military government of the South. It stipulated that Southern states had to ratify the 14th Amendment. They had to give full suffrage to adult male African Americans. If they did such things, they could reenter the Union.
In this way, Congressional Reconstruction was much harsher than presidential Reconstruction had been.
The primary difference was the degree of amnesty and leniency to be extended to the former Confederacy. President Abraham Lincoln's position was that as President he had the pardon power and the obligation to enforce the law, therefore Reconstruction was up to him. Republican members of Congress disagreed; they said that since Congress was charged under the Constitution with guaranteeing every state a Republican form of government, it had the sole power of reconstructing the South.
As early as April, 1863, even before the war had ended, Lincoln proposed his "ten per cent plan" which called for the states in rebellion to form a new government when ten percent of those eligible to vote in the 1860 election swore and oath of allegiance to the U.S. in exchange for a presidential pardon. Excluded from the plan were former Confederate government military officers and government officials, particularly those who had left federal government posts to join the Confederacy. Lincoln was opposed by a group of Republicans determined to reconstruct the South in the image of the North. They were known as "radical republicans." They pushed through Congress the Wade Davis Bill which provided that the southern states could form a new government only after a majority of male citizens swore an oath of past loyalty to the Union, and any new state constitutions must abolish slavery and repudiate Confederate debt. Lincoln pocket vetoed the measure, so it never became law.
Lincoln was assassinated shortly after the end of the war, and Andrew Johnson's position was somewhat similar to Lincoln's. He said that
there is no such thing as reconstruction; Those states have not gone out of the Union. Therefore, reconstruction is not necessary
He was opposed by two prominent Radical Republicans: Thaddeus Stevens of Pennsylvania who said that the former confederate states were now "conquered provinces," and Charles Sumner of Massachusetts who said that the confederate states had committed political suicide and reverted to the status of unorganized territories.
The controversy continued well into Andrew Johnson's presidency, resulting in a failed attempt to remove him from office. It was complicated by refusal of those in the North and South to consider compromise.