In August 2019, he joined Spanish Segunda División club Almería for a club record fee. Benfica signed him in 2020 for a club-record transfer worth €24 million, the most expensive signing in Portuguese football history. In his second season, he won the Bola de Prata for top scorer in the Primeira Liga with 26 goals in 28 games, being named in the Primeira Liga Team of the Year and Primeira Liga Player of the Year. Liverpool then signed him in 2022 for a transfer worth €75 million (£64 million).
After representing Uruguay at various youth levels, Núñez was called up to the senior national team for his first time in 2019. He scored on his international debut against Peru. After missing the 2021 Copa Américadue to an injury, Núñez represented Uruguay at the 2022 FIFA World Cup.