He was elected mayor of Albuquerque in 1997, but in his re-election bid he finished a distant fourth place in the 2001 mayoral election, won by his predecessor Martin Chávez. He ran to reclaim his previous position as Public Lands Commissioner in 2006, narrowly winning the Democratic primary against Ray Powell (who had succeeded him in that office in 1993), but losing the general election to incumbent Republican Lands Commissioner Patrick H. Lyons.[3] He then served as state Natural Resource Trustee until his retirement in 2009.[4]
As Mayor of Albuquerque, Baca also made an effort to lure the Canadian minor league baseball team the Calgary Cannons to Albuquerque with promises of a new $28 million stadium.[5] The effort succeeded and the team was renamed The Albuquerque Isotopes. The move became part of the basis of a 2001 episode of The Simpsons, titled "Hungry, Hungry Homer," which features the owners of the Springfield Isotopes attempted to move their team to Albuquerque.[6][5]