Selected by the Chicago Cubs 318th overall in the 11th round of the 2001 Major League Baseball draft, he made his major league debut on September 23, 2005, against the Houston Astros. He was recalled by the Cubs on July 12, 2007, but only had 1 hit in 7 at-bats. In September 2007, when the Cubs expanded their roster, he joined the team again. This was mainly because, in the minor leagues that year, he batted .353 with 26 home runs and 109 RBI and was named the Pacific Coast League's MVP while playing for the Iowa Cubs. After his call-up in September, Soto had an average of .389. Soto started for the Cubs during the 2007 playoff series against the Arizona Diamondbacks. In game 2 of the series, Soto hit a home run into the left field bleachers at Chase Field, giving the Cubs an early 2–0 lead. The Cubs ended up losing that game, but it further solidified him as the Cubs' full-time catcher going into 2008, with Jason Kendall moving on to Milwaukee as a free agent.

Arguably the best offensive performance in Soto's career came April 30, 2008, in a rout against the Brewers. Soto hit two 3-run homers to account for 6 of the Cubs' 19 RBIs, only a few days removed from a two-game stretch against the Nationals in which he struck out in 8 consecutive at-bats. Soto was voted the National League Rookie of the Month for April 2008 after hitting .341 with 5 home runs, 8 doubles, and 20 RBIs, with an OPS of 1.059. On May 19, 2008, he scored his first career Inside-the-park home run against the Houston Astros. Soto led the early stage of the voting process for the National League's catcher in the 2008 Major League Baseball All-Star Game. He was selected to be the National League's starting catcher in the game. Soto became the first rookie catcher ever to start on the National League All-Star team. Soto is the first Cubs' All-Star rookie to play in the game with at least 14 home runs since Rafael Palmeiro did it in 1987, surpassing the mark when he hit his 15th home run on July 6, 2008. He went 3 for 5 with 7 RBIs in a game on August 26 against the Pittsburgh Pirates.

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