During the 1997 season, Helton hit .280/.337/.484 (batting average, on-base percentage, slugging percentage), with five home runs, in 35 games played. When Rockies first baseman Andrés Galarraga went to the Atlanta Braves in 1998, Helton became the full-time starter at first base for Colorado during the 1998 season. The Rockies named Helton their club representative in 1998, the first time the team ever gave a rookie that role. He hit .315/.380/.530, with 25 home runs and 97 RBI, in 152 games played. Helton led all major-league rookies in average (.315), home runs (25), RBI (97), multi-hit games (49), total bases (281), slugging percentage (.530) and extra base hits (63). He also led all National League rookies in runs (78), hits (167) and on-base percentage (.380). At the time, only Mike Piazza (35), David Justice (28) and Darryl Strawberry (26) had hit more home runs as an NL rookie since 1972, and only Piazza had more RBI (112). Helton finished second to Kerry Wood of the Chicago Cubs in the voting for National League Rookie of the Year. The Tennessee Sports Hall of Fame named Helton its 1998 Professional Athlete of the Year.
The following season, Helton had to spend time on the disabled list again, this time from April 20 – May 4, as he was diagnosed with acute terminal ileitis. He hit .302 with 15 home runs, 81 RBI, 40 doubles, 91 walks and a .404 on-base percentage for the season. He ended the season below .900 in OPS (he had .880 OPS) for the first time since entering the league in 1997 when he only played 35 games that year. Helton finished third on the Rockies roster in 2006 in runs (94), hits (165), doubles (40), total bases (260) and multi-hit games (42).