After signing, Nuñez was assigned to the rookie–level Gulf Coast League Marlins where he compiled a .211/.354/.251 slash line and 28 stolen bases over 48 games.[4] He did not play in a game in 2020 due to the cancellation of the minor league season because of the COVID-19 pandemic.[5] Nuñez began the 2021 season with the Single–A Jupiter Hammerheads, batting .243 with 10 RBI and 33 stolen bases over 52 games.[6] He missed time at the end of the season with a leg injury.[7]
Nuñez split the 2022 season between the High–A Beloit Snappers and Double–A Pensacola Blue Wahoos, accumulating a .251/.384/.317 batting line with two home runs, 41 RBI, and 70 stolen bases across 123 games.[8] He returned to Pensacola in 2023, playing in 125 games and hitting .225/.341/.286 with five home runs, 43 RBI, and 52 stolen bases.[9]