Upon completion of his tour with the Thunderbirds, he was assigned as an F-100 pilot with the 37th Tactical Fighter Wing at Phù Cát Air Base in South Vietnam. On February 1, 1969, he was assigned to Project Commando Sabre (Detachment 1, 416th Tactical Fighter Squadron), known as the "Misty" FACs, a specialized group of high speed forward air controllers trying to stop vehicular resupply traffic down the Ho Chi Minh Trail. He became the tenth commander of Commando Sabre on April 22, 1969, and moved it to the 31st Tactical Fighter Wing at Tuy Hoa Air Base on May 1, when the 37th TFW transitioned to the twin-seat F-4 Phantom II. Rotating out of his command on May 31, 1969 after 98 missions, he served as chief of standardization and evaluation for 31st TFW. McPeak completed a total of 269 combat missions while in Vietnam, was awarded the Silver Star, and remained in-country until 1970, after which he attended the Armed Forces Staff College in Norfolk, Virginia.