Albuquerque spent the remainder of 1983 engaged in operations at sea completing a variety of tests, examinations, certifications, and inspections.
At the beginning of 1984, Albuquerque reentered Electric Boat Shipyard for post-shakedown availability, returning to sea on 15 April. In May, she transited to the Florida coast for weapons and combat systems certifications. During the summer, she participated in a fleet exercise and took part in a midshipman training cruise. In August, Albuquerque began normal operations from her home port. October and November brought extended operations at sea in the Atlantic Ocean, and, in December, she underwent additional repairs at Electric Boat.
Albuquerque began 1985 with sonar training and weapons systems drills in her local operating area. In February, she completed preparations for a two-month patrol that began on 27 February, returning home at the beginning of May. Operations along the East Coast occupied her time until mid-June when Albuquerque went back to sea. Two months later, she returned and took up local duty until November when she cruised to Florida to serve as a school ship for prospective commanding officers. Albuquerque resumed local operations out of her home port in December.
On 14 January 1986, Albuquerque entered Electric Boat Shipyard for a two-month restricted availability. In March, she began alternating between local evolutions and upkeep in her home port until late May. Between 19 May and 14 September, Albuquerque remained at sea, making port calls in Scotland and England. She returned home in mid-September and, after post-deployment standdown, reported to Exuma Sound late in October for sound trials. She returned to Groton briefly at the beginning of November, but put to sea on 4 November to take part in two fleet exercises. Upkeep at New London, Connecticut, took up the period between 24 November and 7 December and an ASW exercise consumed most of December.
The United States Navy confirms that Albuquerque was operating off the coast of Long Island, New York during the evening of 17 July 1996, but had nothing to do with the loss of TWA Flight 800.
In 1999, Albuquerque participated in a six-month Mediterranean cruise as a part of the USS Theodore Roosevelt battlegroup. She fired 10 Tomahawk (TLAM) cruise missiles at targets in Serb-controlled Yugoslavia, setting records for number of TLAMs fired from a Flight-I 688 class submarine, as well as the shortest time from tasking to firing on a target, earning her the nickname of "Sure Shooter". The ship pulled into several liberty ports during this cruise, including Naples, La Maddalena, and Toulon.
In preparation for Engineering Refueling Operation (ERO), USS Albuquerque completed a Dual Media Discharge (DMD). During the shipyard period 22 months in length, the Albuquerque was commended for being the fastest, and most cost effective nuclear reactor refueling operation in history. During this time, CDR Burroughs was relieved of command by CDR Stuart Munch. After completing the major overhaul at Portsmouth Naval Shipyard in Kittery, Maine, USS Albuquerque returned to Groton in early 2003. The rest of 2003 was spent conducing local operations, an ORSE and a weapons system upgrade. Most of 2004 was spent at sea preparing for the ship's first overseas deployment since the shipyard. This included a two month overseas surge deployment with a port call in Rota, Spain.
USS Albuquerque conducted a six month deployment as part of the USS Harry S. Truman Carrier Strike Group from 13 October 2004 to 12 April 2005. The ship made port calls in Scotland, Portugal, Bahrain, Seychelles, and Crete. During this deployment, USS Albuquerque was awarded the Squadron 2 Battle Efficiency Award for 2004. Albuquerque is homeported in Groton, Connecticut, as part of Submarine Group 2.
On 27 June 2005, CDR Robert Douglass relieved CDR Stuart Munsch as Commanding Officer.
In July 2005, Ariel Weinmann, a fire-control technician deserted from Albuquerque and remained at large until he was arrested in early August 2006. In addition to desertion, he was charged with espionage. He allegedly tried to pass sensitive information about Albuquerque to agents of unspecified foreign governments on at least three occasions: in March 2005 in Manama, in October 2005 in Vienna, and in March in Mexico City