Encarnación was invited to spring training by the Marlins in 2020.[7] That year, the Minor League Baseball season was cancelled due to the COVID-19 pandemic, and he did not play in any games.[2] On November 20, 2020, the Marlins added Encarnación to their 40-man roster to protect him from the Rule 5 draft.[8]
Encarnación spent the majority of the 2021 season with the Double–A Pensacola Blue Wahoos, also playing in four games for Jupiter. In 63 games with Pensacola, he hit .222/.308/.400 with nine home runs, 28 RBI, and five stolen bases.[9]
On June 19, 2022, Encarnación made his MLB debut for the Miami Marlins. He hit a grand slam for his first major league hit as the Marlins defeated the New York Mets.[2][3] In 23 games in his rookie campaign, he batted .182/.210/.338 with 3 home runs and 14 RBI.
Encarnación was optioned to the Triple-A Jacksonville Jumbo Shrimp to begin the 2023 season.[10] In 84 games for Jacksonville, he hit .211 with 19 home runs and 54 RBI. On July 21, 2023, Encarnación was removed from the 40-man roster and sent outright to Triple–A.[11] He elected free agency following the season on November 6.[12]
Guerreros de Oaxaca
On January 24, 2024, Encarnación signed with the Guerreros de Oaxaca of the Mexican League.[13] In 26 games for the Guerreros, he batted .366/.439/.989 with 19 home runs and 36 RBI. On May 16, Encarnación was released to pursue an opportunity with an MLB organization. At the time of his release, he was leading the league in home runs, runs scored (33), and OPS (1.428).[14]
San Francisco Giants
On May 16, 2024, Encarnación signed a minor league contract with the San Francisco Giants.[15] In 33 games for the Triple–A Sacramento River Cats, he batted .352/.438/.616 with 10 home runs and 33 RBI. On August 2, the Giants selected Encarnación's contract, adding him to their active roster.[16]