The mechanisms by which exercise benefits human health remain incompletely understood. With the emergence of omics techniques, mapping of the molecular response to exercise is increasingly accessible. Here, we perform an untargeted metabolomics profiling of plasma from a randomized, within-subjects, crossover study of either endurance exercise or resistance exercise, two types of skeletal muscle activity that have differential effects on human physiology. A high-resolution time-series analyses reveal shared as well as exercise-mode-specific perturbations in a multitude of metabolic pathways. Moreover, the analyses reveal exercise-induced changes in metabolites that are recognized to act as signaling molecules. Thus, we provide a metabolomic signature of how dissimilar modes of exercise affect the organism in a time-resolved fashion.