Amaya signed with the Chicago Cubs as an international free agent in July 2015.

Amaya played 2017 with the Eugene Emeralds where he slashed .228/.266/.338 with three home runs and 26 RBIs in 58 games,[2] and spent 2018 with the South Bend Cubs,[3] earning Midwest League All-Star honors[4] and slashing .256/.349/.403 with 12 home runs and 52 RBIs in 116 games.

[6] In 2019, Amaya played for the Myrtle Beach Pelicans,[7] batting .235/.351/.402 with 11 home runs and 57 RBIs over 99 games.

[8] He was selected to play in the Arizona Fall League for the Mesa Solar Sox following the season.

The Cubs optioned Amaya to the Double-A Tennessee Smokies to begin the 2023 season.