Johnston progressed through the academy at Celtic and had loan spells with Vitoria de Guimaraes and West Brom before a permanent transfer to the Black Country in 2024 for £3 million. Last summer, Johnston was close to joining the Brazilian side Flamengo for a fee of around £5 million, but the transfer was unsuccessful due to fan backlash in Rio de Janeiro.

Globo.com reported that a director reached an agreement in the middle of last year to sign Irishman Mikey Johnston from West Bromwich, which plays in the English second division, but Flamengo president Bap cancelled the agreement.

In 2025, a transfer deal for 26-year-old Irish winger Michael Johnston to join Flamengo was nearly completed, with travel plans set for Rio de Janeiro. However, the transfer ultimately did not go through. Concerns were raised by Flamengo's medical department regarding Johnston's history of surgeries and injuries, which sparked significant internal debate about the potential signing. According to an ESPN report, Flamengo's medical team issued a 'yellow light' warning, which halted the deal due to worries about Johnston's ability to maintain consistent performance given his injury history. Despite this setback, Johnston has been performing strongly at West Bromwich in the Championship. His contract with the club is valid until June 30, 2028, and Transfermarkt estimates his market value at €3.00 million.