On 23 July 2013, Bulgaria champions Ludogorets Razgrad replaced coach Ivaylo Petev with Stoycho Stoev, following a 1–0 defeat by Lyubimets on the opening day of the new season.

[1] In the 2013–14 UEFA Europa League he managed Ludogorets to win their group and proceed to the round of 32.

[2] On 13 May 2016, after a meeting with the board of directors, it was announced that Stoev had been released by the club.

[4] In early March 2019, Stoev once again became head coach of Ludogorets Razgrad, taking over from Antoni Zdravkov.

[5] On 25 August 2019, Stoev was fired once again from the club following a 0:0 home draw with Slavia Sofia.