Prior to his retirement, the enlisted members of Air Education and Training Command presented Flowers with the Order of the Sword, the Air Force enlisted force’s highest honor for officer leadership.
When his tour in Vietnam was completed, Flowers was reassigned at Norton Air Force Base, California. While at Norton, he met his wife, who was also serving in the Air Force. Two weeks after they were married, she was transferred to Clark Air Base in the Philippines. Six months later, Flower secured a joint-spouse assignment at Clark. During his tour in the Philippines, Flowers began working toward a college degree. When he returned from his overseas assignment, Flower was retrained as an accounting specialist and assigned to Lackland Air Force Base and then to Charleston Air Force Base, South Carolina.
When he completed his bachelor's degree in 1975, Flowers applied for Air Force Officer Training School and was accepted. Shortly after his acceptance, his wife (who was still enlisted) was reassigned to Iraklion Air Base in Greece. Because there was no guarantee of a joint assignment after officer training, he gave up his officer training slot and went with his family to Greece. In 1976, Flowers finished his master's degree and re-applied to the officer training; however, his application was denied. He applied again in 1977 and was denied again. In the meantime, he was reassigned to Travis Air Force Base, California and select for promotion to master sergeant, the Air Force's third highest enlisted grade. While he was waiting to pin on his new rank, he applied for officer training once again. This time he was accepted.
In July 1985, Flowers was selected for an assignment at Air Force headquarters in The Pentagon. He served three years there, first as a budget officer and the as an executive officer. He attended the Armed Forces Staff College in Norfolk, Virginia from July 1989 until January 1990. After graduating from that joint military education program, he was assigned to headquarters Air Combat Command at Langley Air Force Base, as chief of the command’s Budget Operations Division.
In August 1993, Flowers was selected to attend the Industrial College of the Armed Forces at Fort Lesley J. McNair in Washington, receiving a Master of Science degree from the college in June 1994. This was followed by a budget officer assignment in the office of the Joint Chiefs of Staff at the Pentagon. In December 1996, Flowers was again assigned to headquarters Air Combat Command, where he served as the command’s budget chief. During the assignment, he was promoted to colonel.
In June 1999, Flowers returned to the Pentagon for another tour, this time as director of Budget Programs in the office of the Assistant Secretary of the Air Force for Financial Management and Comptroller. Three years later, he was sent to headquarters Air Education and Training Command at Randolph Air Force Base, Texas as the command’s comptroller. He was then assigned to headquarters United States Special Operations Command at MacDill Air Force Base, Florida. While at MacDill, he was promoted to brigadier general.
Flowers took command of the Air Force Officer Accession and Training Schools in January 2007. He served as the organization's commander until May 2008. During that tour, Flowers was promoted to major general. Flowers was then transferred to Keesler Air Force Base, Mississippi where he took command of 2nd Air Force.
Prior to his retirement, Flowers was awarded the Order of the Sword, the Air Force enlisted force’s highest honor for officer leadership. Several hundred people attend the Order of the Sword ceremony held at the Pentagon’s Airman Hall.
At the time of his retirement, Flowers was the longest serving active duty member in Air Force history. He was also the longest serving African American in the history of the United States Department of Defense. His retirement ceremony was held at on 16 November 2011 at Bolling Air Force Base in Washington. The Secretary of the Air Force, Michael B. Donley and the Assistant Secretary of the Air Force for Financial Management and Comptroller, Jamie M. Morin both attended his retirement ceremony.