Shebalkov fought in the retreat to the east after Operation Barbarossa, the German invasion of the Soviet Union. He fought in the defense of Kremenchug and Pyriatyn, as well as Poltava Oblast and Kharkov Oblast. In December 1941, Shebalkov fought in the Battle of Rostov. During the summer of 1942 he fought in the Soviet retreat to the east after the German offensive Case Blue. Shebalkov's unit ended in the Battle of Stalingrad, in which he was deputy commander of a reconnaissance platoon with the 15th Motor Rifle Brigade. He fought in the Battle of Kursk and in Ukraine and Romania. Serving in a unit with the 2nd Guards Tank Army, Shebalkov fought in Operation Bagration and the capture of Radom, Lublin, Dęblin, and Garwolin. He was wounded three times. In 1944 he became a Communist Party of the Soviet Union member. On 26 September he was awarded the Medal "For Courage" for actions between March and June.