2006 as the Mariners fell to the host Chicago White Sox, 11–7. He hit a fifth-inning single off Mark Buehrle, driving in Raúl Ibañez. His final career at-bat was September 29, 2006. At age 37, playing for the Seattle Mariners in a 6–5 loss to the Texas Rangers, he pinch hit for Ben Broussard and struck out against C. J. Wilson. Later career Pérez joined ESPN's Baseball Tonight 2006 postseason coverage along with then-current player Vernon Wells, and former players Tino Martinez and Eric Byrnes. Pérez worked as an analyst for "Baseball Tonight" through 2011 and also served as an analyst for ESPN Deportes' "Béisbol Esta Noche." In 2007, he provided commentary for the NCAA baseball regionals, the Triple-A All-Star Game and the Little League World Series regionals. He speaks both English and Spanish fluently. In late 2007, three months after the Puerto Rican winter baseball league was cancelled after 69 seasons, Pérez returned to Puerto Rico and announced his founding of the Winter Training Program (WTP) for both professional and amateur players in an effort to return pro baseball back to the island. The program was sponsored by the government municipality of San Juan, Major League Baseball, and private donors. In 2008 and 2009, Pérez was manager of Leones de Ponce in Puerto Rico. He was named 2008 Manager of the Year in the Puerto Rico Baseball League, leading the team to the league title. While serving as a special assistant to the baseball operations department of the Cleveland Indians, on June 8, 2011, Pérez was named hitting coach of the Miami Marlins, replacing John Mallee, a position he held until manager Ozzie Guillén and most of his staff were let go shortly after the 2012 season. He managed the team representing Colombia in the World Baseball Classic Qualifying Round in 2013, finishing with a 1–2 record. He served as the Houston Astros bench coach under manager Bo Porter during the 2013 season. For 2014, he was named the Astros first base coach, but he resigned that position in early January 2014 to spend more time with family. On February 11, 2014, ESPN announced that Pérez had rejoined the network as a studio and game analyst. During the winter of 2014–2015, Pérez served as the manager of the Santurce Crabbers in the Puerto Rican Winter League. The Crabbers won the league championship and participated in the Caribbean World Series.