Runners who experience insufficient recovery time after training demands may have increased injury risk. Training and exercises can induce fatigue and altered movement patterns, which may best be assessed by examining the dynamics of the movement structure during a sports-related task. This crossover experimental study investigated the immediate and prolonged effects of exercise at different intensities on lower-limb joints and coordinative patterns during a 60-second single-leg squat task in 30 healthy runners. Joints (ankle, knee, hip) and coordination (ankle-knee, knee-hip continuous relative phase) angles were assessed between measurement times (pre, post, post24h, post48h) and protocols (moderate- and high-intensity run, control). A Statistical Parametric Mapping (SPM) one-way repeated measures ANOVA analyzed the joints and coordination time-normalized curves. Additionally, the entropy (i.e., regularity) of the entire time series was assessed by a two-way ANOVA. Lower ankle-knee coordination entropy was observed immediately after running protocols (moderate-intensity, −17.6 %, p = 0.003, η²ₚ = 0.21;​ high-intensity, −18.6 %, p = 0.001, η²ₚ = 0.22) and was also observed individually on the ankle and knee at post48h (p < 0.001, η²ₚ = 0.10). . No time or protocol effects were observed for SPM analysis. Runners demonstrated more regular (lower entropy) ankle-knee coordination after running protocols, which is related to a less adaptative pattern. In addition, increased regularity was observed on ankle and knee joint angles 48 h after protocols, suggesting an ongoing recovery process. The analysis of time-normalized kinematics was not sensitive to detect the effect of running on movement. Therefore, evaluating the coordination regularity during a single-leg test helped track the effect of exercise and fatigue, even without maximal effort.