Movement dynamics during running was previously characterized using a trunk-mounted accelerometer, and were associated with a history of overuse injuries. However, it remains unknown if these measures are also linked to the development of overuse injuries. The aim of this study was therefore to determine how movement dynamics alter in response to fatigue, and the possible link with developing lower-leg overuse injuries during a six-month follow-up period. Two hundred and eight movement science university students completed a 12-min all-out run while wearing a trunk-mounted accelerometer. Dynamic stability, dynamic loading and spatiotemporal measures were extracted from the accelerometer. Participants sustaining an injury within the 6-month period demonstrated significantly higher RMS ratio values in the vertical direction and lower RMS ratio values in the anteroposterior direction, and lower impact acceleration values in the anteroposterior direction in an unfatigued state compared to the uninjured group. They also demonstrated an increase in dynamic loading in the horizontal plane during the run. In addition, with running fatigue both groups exhibited changes in dynamic stability and loading measures. These results show the potential of using a single trunk-mounted accelerometer to detect changes in movement dynamics that are linked to lower-leg overuse injuries.