On March 3, 1847, McKinstry was appointed captain staff and assistant quartermaster general. Although he was a quartermaster, McKinstry was awarded a brevet appointment as a major in the Regular Army (United States) for gallant and meritorious conduct after taking command of a company of volunteers at the Battles of Contreras and Churubusco, to rank from August 20, 1847. McKinstry was an original member of the Aztec Club of 1847, which was founded as a military society of officers who served with the United States Army in the Mexican–American War.