At Lincoln's inauguration on March 4, 1861, the Turners formed Lincoln's bodyguard, and a sizable garrison of Union troops was always present, ready to protect the president and the capital from rebel invasion.

Lincoln's actual position on freeing enslaved African-Americans is controversial today, despite the frequency and clarity with which he stated it both before his election to president (i.e. Lincoln-Douglas Debates of 1858) and after (see Lincoln's First Inaugural) He stated his position forcefully and succinctly in a letter to Horace Greeley of August 22, 1862.

Also revealing was his letter a year later to James Conkling of August 26, 1863, which included the following excerpt:

You say you will not fight to free negroes. Some of them seem willing to fight for you; but, no matter. Fight you, then exclusively to save the Union. I issued the proclamation on purpose to aid you in saving the Union. Whenever you shall have conquered all resistence to the Union, if I shall urge you to continue fighting, it will be an apt time, then, for you to declare you will not fight to free negroes.

I thought that in your struggle for the Union, to whatever extent the negroes should cease helping the enemy, to that extent it weakened the enemy in his resistence to you. Do you think differently? I thought that whatever negroes can be got to do as soldiers, leaves just so much less for white soldiers to do, in saving the Union. Does it appear otherwise to you? But negroes, like other people, act upon motives. Why should they do any thing for us, if we will do nothing for them? If they stake their lives for us, they must be prompted by the strongest motive?even the promise of freedom. And the promise being made, must be kept.

Lincoln is often credited with freeing enslaved African-Americans with the Emancipation Proclamation, though this only freed the slaves in areas of the Confederacy not yet controlled by the Union; in occupied and northern territories, slaves were not freed. However, as the proclamation made abolishing slavery in the rebel states an official war goal it did become the impetus for the enactment of the 13th and 14th Amendments of the United States Constitution which respectively abolished slavery and established the federal enforcement of civil rights.

He showed tremendous leadership to the Union populace during the war as evidenced by the Gettysburg Address, a speech dedicating a cemetery of union soldiers from the Battle of Gettysburg in 1863. While most of the speakers e.g. Edward Everett - at the event spoke at length, some for hours, Lincoln's few choice words resonated across the nation and across history, defying Lincoln's own prediction that "The world will little note, nor long remember what we say here." While there is little documentation of the other speeches of the day, Lincoln's address is regarded as one of the great speeches in history.

The war was a source of constant frustration for the president, and it occupied nearly all of his time. After repeated frustrations with General George McClellan and a string of other unsuccessful commanding generals, Lincoln made the fateful decision to appoint a radical and somewhat scandalous army commander: General Ulysses S. Grant. Grant would apply his military knowledge and leadership talents to bring about the close of the Civil War.

When Richmond, the Confederate capital, was at long last captured, Lincoln went there to make a public gesture of sitting at Jefferson Davis's own desk, symbolically saying to the nation that the President of the United States held authority over the entire land. He was greeted at the city as a conquering hero by freed slaves whose sentiments were epitomized by one admirer's quote, "I know I am free for I have seen the face of Father Abraham and have felt him."

The reconstruction of the Union weighed heavy on the President's mind. He was determined to take a course that would not permanently alienate the former Confederate states.

In 1864, Lincoln was the first and only President to face a presidential election during a civil war. The long war and the issue of emancipation appeared to be severely hampering his prospects and an electoral defeat appeared likely against the Democratic nominee, George McClellan. However, a series of timely Union victories shortly before election day changed the situation dramatically and Lincoln was reelected.

During the Civil War Lincoln held powers no previous president had wielded; he suspended the writ of habeas corpus and frequently imprisoned Southern spies and sympathizers without trial. On the other hand, he often commuted executions.