The Twins signed Santana as an undrafted free agent in December 2007. In November 2012, the Twins added Santana to the 40 man roster in order to protect him from the teams who wanted him.

Santana was called up to the major leagues for the first time on May 2, 2014. After a solid start to his career, Santana was placed on the 15-day disabled list on June 27, 2014. Santana finished the season splitting time between center field and shortstop, finishing the season with a .319 AVG in 101 games for the Twins. He also hit 7 home runs along with 20 stolen bases.

Santana finished 7th in Rookie of the Year voting, leading all MLB nominees in batting average (.319) and stolen bases (20). Additionally, Santana's rookie year batting average of .319 is a Twins franchise record (minimum 130 ABs).

Santana began the season as the Twins' shortstop. He regressed throughout the season, hitting just .215 for the season with no home runs.

Santana continued to see his playing time decrease due to other players on the team performing better. Despite this, Santana continued to see playing time at shortstop but an injury cost him half a season.

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