Aerobic exercise helps to maintain cardiovascular health in part by mitigating age-induced arterial stiffening. However, the long-term effects of exercise regimens on aortic stiffness remain unknown, especially in the intimal extracellular matrix layer known as the subendothelial matrix. To examine how the stiffness of the subendothelial matrix changes following exercise cessation, mice were exposed to an 8 week swimming regimen followed by an 8 week sedentary rest period. Whole vessel and subendothelial matrix stiffness were measured after both the exercise and rest periods. After swimming, whole vessel and subendothelial matrix stiffness decreased, and after 8 weeks of rest, these values returned to baseline. Within the same time frame, the collagen content in the intima layer and the presence of advanced glycation end products (AGEs) in the whole vessel were also affected by the exercise and the rest periods. Overall, our data indicate that consistent exercise is necessary for maintaining compliance in the subendothelial matrix.