[2] He made his debut in the Cubs system for the Low-A Boise Hawks in 2009 after recovering from Tommy John surgery.

[6] On January 7, 2011, Lee was traded to the Tampa Bay Rays along with fellow prospects Chris Archer, Brandon Guyer, Robinson Chirinos and Cubs outfielder Sam Fuld for pitcher Matt Garza, outfielder Fernando Perez and minor league pitcher Zac Rosscup.

[7][8] Lee started the 2011 season with the High-A Charlotte Stone Crabs, leading the team in AVG (.318) and SLG (.443), and earned a mid-season promotion to the Double-A Montgomery Biscuits, where he went 19-for-100 in 24 games.

He was activated on April 22 and spent the remainder of the year with the team, posting a .203/.287/.276 slash line with 4 home runs and 23 RBI.

On November 18, 2015, Lee signed a minor league contract with the San Francisco Giants organization that included an invitation to Spring Training.

Lee logged a .265/.344/.377 batting line with Sacramento before exercising a June 1 opt-out clause in his deal and electing free agency.

At the time of the draft, Lee had accumulated 23 homers, 209 RBIs, 169 steals and averaged .269 in 678 games from his eight seasons in the minor leagues with the Cubs, Rays, and Giants organizations.