Former England, Chelsea and Juventus forward Aluko was appointed as sporting director at Angel City in May 2021, after doing the same job at Aston Villa.
The Los Angeles-based outfit, who had their first National Women's Soccer League season in 2022, last August said Aluko was to "evolve into the new role of director of recruitment, a key role she has played since joining the team".
A statement on Twitter regarding the 35-year-old's departure said: "Angel City and Eniola Aluko have mutually agreed to part ways.
"She is returning to the UK to be close to her family, focus on her broadcasting career, and other opportunities.
"We are grateful to Eni for her contributions to our historic inaugural season."
Angel City, who were co-founded by actor Natalie Portman and have singer Christina Aguilera among their investors, finished eighth in the NWSL last year.