Recent findings suggest that an acute physical exercise modulates the temporal features of the EEG resting microstates, especially the microstate map C duration and relative time coverage. Microstate map C has been associated with the salience resting state network, which is mainly structured around the insula and cingulate, two brain nodes that mediate cardiovascular arousal and interoceptive awareness. Heart rate variability (HRV) is dependent on the autonomic balance; specifically, an increase in the sympathetic (or decrease in the parasympathetic) tone will decrease variability while a decrease in the sympathetic (or increase in the parasympathetic) tone will increase variability. Relying on the functional interaction between the autonomic cardiovascular activity and the salience network, this study aims to investigate the effect of exercise on the resting microstate and the possible interplay with this autonomic cardiovascular recovery after a single bout of endurance exercise. Thirty-eight young adults performed a 25-min constant-load cycling exercise at an intensity that was subjectively perceived as "hard." The microstate temporal features and conventional time and frequency domain HRV parameters were obtained at rest for 5 min before exercise and at 5, 15, 30, 45, and 60 min after exercise. Compared to the baseline, all HRV parameters were changed 5 min after exercise cessation. The mean durations of microstate B and C, and the frequency of occurrence of microstate D were also changed immediately after exercise. A long-lasting effect was found for almost all HRV parameters and for the duration of microstate C during the hour following exercise, indicating an uncompleted recovery of the autonomic cardiovascular system and the resting microstate. The implication of an exercise-induced afferent neural traffic is discussed as a potential modulator of both the autonomic regulation of heart rate and the resting EEG microstate.