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.[5] He was selected to play in that year's All-Star Futures Game.[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. He was also selected to the All-Star Futures Game for the second consecutive year.[8] He was selected to play in the Arizona Fall League for the Mesa Solar Sox following the season.[9]
Following the 2019 season, the Cubs added Amaya to their 40-man roster.[10] He did not play a minor league game in 2020 due to the cancellation of the minor league season caused by the COVID-19 pandemic.[11] He underwent Tommy John surgery during the 2021–22 offseason.
The Cubs optioned Amaya to the Double-A Tennessee Smokies to begin the 2023 season.[12] In 13 games for Tennessee, he hit .273/.411/.659 with four home runs and eight RBIs. On May 2, 2023, the Cubs promoted Amaya to the major leagues for the first time.[13]