In June 1999, Stoyanov joined Cherno More Varna for an undisclosed fee. He settled well and became an integral part of the Cherno More team that won promotion to A PFG in 2000, after a 6-year absence. He made his debut on 7 August 1999, in a 1–0 home victory over Lokomotiv Plovdiv. His first goal came on 18 September, in a 3–1 defeat away to Vidima-Rakovski. During his first three seasons at Ticha Stadium, he plays as a right side midfielder and a right winger.