The breed is best known for its unique gait, known as the fox trot,a four-beat diagonal gait in which the horse appears to walk with its front legs and trot with its hind. The gait, however, is not a mixed patter of footfalls, it has a clear pattern of diagonal foot movement where the front foot hits the ground split-second before the opposite rear foot. The head shakes in unison with the rhythm of the gait. The tail perfectly balances the movements of the head. Because the horse has a four-beat motion rather than a two-beat trot, the gait is easy to sit. It is accompanied by an up and down head nodding. The horses, unlike some other gaited breeds, do not have high-stepping action, but rather a very smooth, comfortable ride. The fox trot can be maintained for great stretches of time, reaching speeds up to 12 mph. A Fox Trotter can also perform a speed fox trot which goes 12-18 mph. The Fox Trotter also performs the flat-footed walk and the regular canter. Some Fox Trotters can also perform various lateral ambling gaits, such as the running walk or singlefoot. However, the fox trot is considered a more surefooted gait.

The Missouri Fox Trotter is also known for its stamina and soundness. The horses have a willing and gentle disposition, and are very surefooted. They are generally medium-height, between 14.2 and 16.2 hands. They come in most equine coat colors, including most solid colors, and also including most pinto spotting patterns, but do not exhibit Appaloosa coloring.