Volunteering for the Red Army at the outset of the Russian Civil War, Trubnikov was first appointed as a military officer for his hometown. In May 1919 he was sent to the front, commanding a platoon, a company, and then a battalion in the 28th Rifle Regiment of the 7th Rifle Division. He fought on the Eastern Front against the White Army troops of Alexander Kolchak in the Votkinsk and Izhevsk districts, but in the summer the regiment was urgently transferred to the Southern Front, where Anton Denikin was advancing on Moscow. In August he became deputy commander and then commander of the 55th Rifle Regiment, also of the 7th Division, and fought in battles around Oboyan and Sudzha. From October to November he was involved in the Orel–Kursk operation, a decisive Soviet victory in which the Red Army regained the initiative. During the Polish–Soviet War he commanded a regiment and then the 20th and 19th brigades of the 7th Division. In the autumn of 1920 he fought against Stanisław Bułak-Bałachowicz near Ovruch and then against the anarchist army of Nestor Makhno near Zolotonosha.