Abraham Lincoln got underway on 20 March 1961 for shakedown and weapons testing at Cape Canaveral, Florida, and returned to Portsmouth Naval Shipyard on 1 June for post-shakedown repairs.

She left Portsmouth Naval Shipyard on 17 July 1961 to return briefly to Cape Canaveral for further testing and then proceeded to Charleston, South Carolina, for a final loadout.

She alternated periods of upkeep at Holy Loch alongside Proteus or submarine tender USS Hunley with deterrent patrols from that port.

This work was completed on 3 June 1967, and Abraham Lincoln returned to her base at Holy Loch and resumed her schedule of deterrent patrols.

In early March 1972, Abraham Lincoln departed for the United States and arrived at Naval Submarine Base New London at Groton, Connecticut, on 25 April 1972.

Abraham Lincoln made a brief visit to Fort Lauderdale, Florida, transited the Panama Canal on 1 June, sailed to Bangor, Washington, to offload her missiles, then pushed on to San Francisco.

She retransitted the Panama Canal on 26 July 1974 and proceeded to her new home port, Pearl Harbor, Hawaii, where she arrived on 10 September 1974 to become part of CINCPAC Fleet and Squadron 15.