Musayev passed his UEFA Pro Licence exam in the summer of 2020 and was officially registered with the league as Krasnodar's manager on 20 June 2020.

He resigned from Krasnodar on 3 April 2021 following a string of bad results after 2020–21 season was resumed after a winter break, including a biggest ever club defeat (1–6 to FC Spartak Moscow away) and a biggest ever home loss (0–5 to FC Akhmat Grozny).

[3] On 1 February 2024, Sabah announced that Musayev had left his role as head coach after his resignation had been accepted.

[4] On 14 March 2024, Krasnodar announced the return of Musayev as head coach of the club, on a contract until the end of the season.

[6] Krasnodar began the 2024–25 Russian Premier League season with 14 unbeaten games, including a club-record streak of 11 wins, taking the top spot in the standings.