In 1999, he graduated from the Combined Arms Academy, and in September of the same year, Stvolov fought in Dagestan as commander of the 503rd Motor Rifle Regiment. He led regiment during the battles in Karamakhi, Chabanmakhi, Ishcherskaya, and Grozny. He was wounded 4 times during the war. In subsequent engagements, Stvolov served as chief of staff of the "West" military group and deputy commander of the 205th Motor Rifle Brigade. In March 2000, Stvolov took part in the assault on Komsomolskoye. By the decree of the President of Russia on 9 September 2000, Sergei Stvolov was awarded the title of Hero of the Russian Federation with the Golden Star medal for his activities during the Chechen Wars.