[3] In 2013 he played in the rookie–level Gulf Coast League for the Gulf Coast League Nationals,[2] who that year finished their regular season with a record of 49–9, giving them the highest winning percentage (.845) for a full regular season ever achieved by a minor-league baseball team based in the United States.

[2] Bautista spent 2014 with the Single–A Hagerstown Suns in the South Atlantic League,[2] hitting .290 with five home runs, 54 RBIs, and 69 stolen bases.

[2] Bautista advanced to the Double–A Harrisburg Senators in the Eastern League for the 2016 season,[2] hitting .282 with four home runs, 39 RBI, and 56 stolen bases.

[3] He had made 45 plate appearances for Syracuse, batting .429 with a .966 on-base-plus-slugging percentage (OPS)[16] when, on April 24, the Nationals called him up to the major leagues.

[17] He appeared in nine games, usually as a late–game replacement or a pinch–runner, made one start, and went 0–for–6, striking out once and scoring a run[3][16] before the Nationals optioned him back to Syracuse on May 7 to make room on their 25–man roster when they activated right–handed relief pitcher Shawn Kelley from the 10–day disabled list.

[16] He ended his season with an overall .303 batting average in the minor leagues, with three doubles, a triple, a home run, seven RBI, and six stolen bases for the year.

[20] In 2019, Bautista played for Double–A Harrisburg, Single–A Hagerstown, and Low–A Auburn, slashing .182/.256/.255 with two home runs and nine RBI across 29 games between the three affiliates.