Bautista made his professional debut for the Dominican Summer League Marlins in 2013, logging a 2.73 earned run average (ERA) with 17 strikeouts in 11 appearances.

Bautista split the 2019 season between the Low-A Aberdeen IronBirds and the Single-A Delmarva Shorebirds, accumulating a 3.44 ERA with 48 strikeouts in 26 total appearances between the two affiliates.

[12] Bautista was named the AL Reliever of the Month for April 2023 after going 7-for-7 in save chances, striking out 25 batters in 13.2 innings pitched, and posting a 46.4% whiff rate.

[13] On May 20, Bautista pitched the ninth and tenth innings of an extra-inning victory against the Toronto Blue Jays, recording a career-high five strikeouts in the appearance.

In addition, on February 9, 2024, Bautista underwent a debridement and an ulnar nerve transposition in the same elbow that had Tommy John months before.