Electrical neuroimaging is a promising method to explore the spontaneous brain function after physical exercise. The present study aims to investigate the effect of acute physical exercise on the temporal dynamic of the resting brain activity captured by the four conventional map topographies (microstates) described in the literature, and to associate these brain changes with the post-exercise neuromuscular function. Twenty endurance-trained subjects performed a 30-min biking task at 60% of their maximal aerobic power followed by a 10 km all-out time trial. Before and after each exercise, knee-extensor neuromuscular function and resting EEG were collected. Both exercises resulted in a similar increase in microstate class C stability and duration, as well as an increase in transition probability of moving toward microstate class C. After the first exercise, the increase in class C global explained variance was correlated with the indice of muscle alterations (100 Hz paired stimuli). After the second exercise, the increase in class C mean duration was correlated with the 100 Hz paired stimuli, but also with the reduction in maximal voluntary force. Interestingly, microstate class C has been associated with the salience resting-state network, which participates in integrating multisensory modalities. We speculate that temporal reorganization of the brain state after exercise could be partially modulated by the muscle afferents that project into the salience resting-state network, and indirectly participates in modulating the motor behavior.