Córdoba made the Padres' 2017Opening Day roster.[4] At 21 years old, he had never previously played above Rookie League ball.[5] He hit his first major league home run on April 18, 2017, versus Jaime García in the seventh inning of 5−4 loss to the Atlanta Braves at SunTrust Park.[6] Córdoba was batting as high as .310 as of June 2, but he slumped afterward, and lost playing time as a result.[7] Cordoba made a total of 42 starts in 2017, 24 in left field, 15 at shortstop, 2 in center, and 1 in right, but only had 56 plate appearances after the All-Star break.[5] Cordoba made 11 of his starts in left in May after Travis Jankowski went down with a foot injury, but he was displaced by José Pirela, who came up in early June. He saw more playing time at shortstop in June, but the Padres chose to stay with Erick Aybar, and then Dusty Coleman when Aybar was on the disabled list.[8] Cordoba finished the season with a .208/.282/.297 batting line and 4 home runs in 202 at-bats.
Córdoba missed the beginning of the 2018 season with a concussion, and did not make an appearances in the majors after struggles in High-A with the Lake Elsinore Storm. On November 20, 2018, Córdoba was designated for assignment by the Padres.[9] On November 26, Córdoba was outrighted to Triple-A El Paso.[10] Córdoba spent the 2019 season in Lake Elsinore, batting .301/.367/.412 with career-highs in home runs (5) and RBI (43) in 105 games. Córdoba did not play in a game in 2020 due to the cancellation of the minor league season because of the COVID-19 pandemic.[11] After the 2020 season, he played for Panama in the 2021 Caribbean Series.
Cincinnati Reds
On December 1, 2021, Cordoba signed a minor league contract with the Cincinnati Reds.[12] He was released on June 19, 2022.[13]
Algodoneros de Unión Laguna
On July 1, 2022, Córdoba signed with the Algodoneros de Unión Laguna of the Mexican League.[14] In 30 games, he slashed .431/.478/.647 with six home runs, 22 RBI, and 12 stolen bases.
Córdoba played in 85 games for Laguna in 2023, hitting .338/.421/.444 with four home runs, 42 RBI, and 18 stolen bases. In 2024, he made 84 appearances for the Algodoneros, batting .304/.412/.421 with four home runs, 29 RBI, and 10 stolen bases.