However, Weber was released by the Reds after the season. He felt the Reds "treated [him] like a non-prospect". In 2001, Weber played independent league baseball for the Canton Crocodiles of the Frontier League. He batted .307 with a .382 OBP, .559 SLG, 18 home runs and 69 RBI in 84 games, being named to the Frontier League post-season All-Star team. He led the Frontier League in home runs and triples. Canton sold Weber to the Fargo-Moorhead Redhawks of the independent Northern League in 2002, where he hit .296 with a .351 OBP, .501 SLG, and 30 doubles for Fargo-Morehead, placing fourth in the league in doubles. Back with Fargo-Moorhead to open 2003, he batted .309 with a .408 OBP and .520 SLG through 52 games, as the team went on to win the Northern League championship. However, in July 2003, the Oakland Athletics organization purchased Weber's contract from Fargo-Moorhead. With the Athletics organization, Weber hit .361 with a .394 OBP, .626 SLG, seven home runs and 48 RBIs in 35 games with the Single-A Advanced Modesto A's of the California League for the remainder of that year. In 2004, he hit .280 with a .356 OBP, .458 SLG, 15 home runs and 68 RBI in 111 games with the Double-A Midland RockHounds of the Texas League, and hit .341 with a .383 OBP, .568 SLG, two home runs and 12 RBI in 12 games with the Triple-A Sacramento River Cats of the Pacific Coast League (PCL), helping the River Cats win the PCL championship. Weber signed with the Los Angeles Dodgers after the 2004 season as a free agent. In 2005, he hit .300 with a .369 OBP, .456 SLG, 11 home runs and 68 RBIs in 117 games with the Double-A Jacksonville Suns of the Southern League. He was ninth in the league in batting average and led the league's outfielders in assists (19) and double plays (7). With Weber, Jacksonville won the Southern League championship, his third year in a row as a member of a championship-winning team. During the season, Weber received a 15-game suspension for violating minor league baseball's drug policy. Weber, who failed a drug test administered in August 2004, said he had taken thermogin, a supplement that contained the banned substance ephedrine, and denied taking steroids.