The slick-fielding Perez first platooned with and then supplanted Walt Weiss with the Colorado Rockies, and in just his second season (1998) played the full 162 games at shortstop. Perez made significant strides offensively the following year, no doubt aided by the thin air in Coors Field, when he drove in 70 and slugged 12 homers, though a slump at the end of the year ruined his bid for 200 hits.
Accustomed to hitting from the second or sixth spot in the batting order, Perez was shifted to the number one slot in ’99 when Darryl Hamilton and Mike Lansing faltered leading off. Though he hit decently, his on-base percentage was just .297 that year, hampered by his poor plate discipline. In 2000, manager Buddy Bell shifted Perez down to his more comfortable spots at second, sixth, and seventh, where he was more relaxed at the plate. His fielding was as sharp as ever that year, and the Dominican-raised shortstop brought home his first Gold Glove Award, with perennial winner Rey Ordonez sidelined for much of the year.
Amidst a contract extension dispute and the impressive middle infielder Juan Uribe excelling in the minors, the Rockies dealt Perez in July 2001 to the Kansas City Royals in a three-way deal that netted them prospect Jose Ortiz from the Oakland Athletics.