In the summer of 1919 Yakir was sent to Ukraine to command the 45th rifle division, and in August 1919 he became the commander of the Southern Group of the 12th army which included the 45th and 58th rifle divisions. Both divisions were surrounded in Odessa by the White forces. Yakir undertook one of the most remarkable Civil War military operations. He breached the encirclement and led his forces through the enemy rear for a distance of 400 kilometers to join the Red Army in Zhitomir. Like other Bolshevik commanders who did not have military education, he was assisted in this operation by former tsarist army officers on his staff but this fact does not negate his own role in planning and leading the campaign. For this campaign he received his second Order of the Red Banner, and both of his divisions received Red Banners of Honor. Yakir took part in actions against the White forces of Yudenich in defense of Petrograd, in suppression of Ukrainian anarchist partisans of Nestor Makhno and in the Polish-Soviet War. He was awarded a third Order of the Red Banner and became one of the most decorated Red Army commanders.
After the war Yakir commanded army formations in Ukraine. Yakir was a close associate of Mikhail Frunze and belonged to his inner circle of innovative Red Army officers who assisted Frunze in starting far-reaching military reform. Among these reformers was Mikhail Tukhachevsky who became Yakir's friend. In April 1924 Yakir was appointed a head of Main Directorate of Military Academies of the Red Army and simultaneously editor of major military periodical devoted to development of military theory "Voennyi Vestnik."
In November 1925, after Frunze's death Yakir was appointed commander of the most powerful territorial formation of the Red Army, the Ukrainian military district. Yakir in close coordination with Tukhachevsky and other reformers made his district into a laboratory of wide-ranging experiments in strategy, tactical, operational techniques, army formations and equipment. In training his troops, Yakir encouraged his officers' initiative and ability to make their own judgments. In 1928-1929 Yakir studied at the Higher Military Academy in Berlin, this was possible because the intensive military cooperation between the Soviet Union and Germany. Yakir's innovative approaches to the military art impressed his German colleagues; German Field Marshal of WWI fame Paul von Hindenburg praised him as one of the most talented military commander of the post-WWI era.
After returning to his district Yakir continued military reform. He was one of the creators of the first large tank and air force formations in the world. Not a military theorist in his own right, Yakir strongly supported Tukhachevsky's endeavor in developing the theory of deep operations. Military historians across the world now consider this theory the most outstanding theoretical innovation in the entire history of military art. In 1934 Yakir requested that Tukhachevsky would be appointed to conduct advanced courses on operational theory for high-ranking officers of the Red Army General Staff and commanders of military districts. He did it even though he knew about Stalin's dislike of Tukhachevsky. In retribution Stalin instructed his crony Kliment Voroshilov who was a Peoples Commissar of Defense to bar Yakir from membership in the prestigious Advisory Council of the Defense Commissariat. In 1935 in order to diminish Yakir's power Ukrainian military district was divided into two new districts, Kiev under Yakir's command and Kharkov.
In 1935 Yakir conducted famous Kiev military maneuvers with forces of Kiev and Kharkov military districts. The major aim of these maneuvers was to test the theory of deep operations and the latest technology. 65,000 troops, including 1,888 paratroopers, 1,200 tanks and 600 aircraft participated in these maneuvers. These were first maneuvers in the world that used combined operations of large tank, airforce and airborne formations. The troops acted on front of 250 kilometers and a depth of 200 kilometers. The representatives of major world armies attended the maneuvers. The British General Archibald Wavell reported to his government: "If I had not witnessed this myself I would never have believed such an operation possible." The German Wehrmacht copied Soviet innovations in preparation for WWII. The reform started by Frunze and continued by Yakir, Tukhachevsky and many other commanders made the Red Army into most advanced army in the world. It is a common opinion of the Western military experts that if German-Soviet war had started in 1937 before the Stalin purge the Red Army would have been more than a match for the Germans. During these years Yakir regularly gave lectures to the Red Army General Stuff Academy, informing the students about newest developments in military affairs. In 1935 he received the second highest Soviet military rank of that time Komandarm of first rank.
Stalin who was consolidating his power over country, approved Yakir's appointment to Ukrainian Military District in 1925, but he did not trust him fully and instructed his political ally Lazar Kaganovich to became friend with Yakir and to report about his activities. Yakir as a true believer in the Communist cause was actively involved in internal politics. He was member of the party Central Committee in Moscow and member of the Politburo of the Communist Party of Ukraine. While ingenious and independent in his thinking as military commander, in Soviet politics he was a docile party member and followed the party Stalinist line. During the famine in Ukraine caused by Stalin's "forced collectivization" of agriculture during 1932-1933, Yakir was alarmed by the tragedy and approached Stalin with a request to soften official policies. Stalin was outraged and instructed Kaganovich to advise Yakir to limit his activities to his party assignment which was military service. Yakir obeyed. As a party member he lacked the power of conviction and independent thinking to defy Stalin.
His blind obedience did not spare Yakir. Stalin would not allow to his military commanders any independent thinking even in area of their professional expertise. While on the surface Stalin's attitude toward Yakir was friendly, the dictator could not tolerate people like Yakir in the Stalinist totalitarian state. With start of the Great Purge in 1936 NKVD arrested many close associates and subordinates of Yakir. Yakir was one of few top Soviet commanders who appealed to Stalin, claiming the innocence of these officers. Yakir's appeals alienated Stalin even more and Yakir was marked for persecution. To remove Yakir from his power base in June 1937 Stalin sent him to command the Leningrad military district. During the Great purge it was a clear sign of forthcoming persecution.
In 1937 the NKVD accused him of participating in Trotskyist Anti-Soviet Military Organization. Charged with, among other things, being a Nazi agent, he maintained his innocence both in correspondence to Stalin and at his trial, but Stalin wrote on his letter: "Rascal and prostitute". Voroshilov and Molotov added: "A perfectly accurate definition". Kaganovich wrote: "The only punishment for the scoundrel, riffraff and whore is death penalty". Yakir was executed together with Tukhachevsky and several other outstanding Soviet officers immediately after the trial that was held on June 11, 1937. His wife was subsequently arrested and executed, as were several of his relatives. His son, then fourteen years old, was arrested shortly after his father's execution and spent a number of years in prison camps.
After Yakir's execution the purge wiped out large number of the officers who had served under him. Much of Yakir's work, including his reforms and preparations for guerrilla activities in the event of an invasion of Ukraine were dismantled. When Germany invaded the Soviet Union in June 1941 the Red Army was incapable of modern warfare and unprepared to face an enemy who used military art which Yakir and other Soviet innovators pioneered. The Soviets suffered terrible defeats and huge human and territorial losses before mastering modern operational approaches and tactics. Yakir's disciples who survived the purge used the experiences which they had gained under Yakir to make a vital contribution to Soviet victory over Germany. Among them were Chief of the General Staff of the Red Army Aleksei Antonov, Front commanders Andrei Yeremenko and Ivan Chernyakhovsky, and Army commander Aleksandr Gorbatov.