Exercise promotes health by engaging complex signalling pathways to promote insulin sensitivity, however the mechanisms by which this occurs remain unclear. Here we performed high-throughput phosphoproteomics of human skeletal muscle from both exercised and non-exercised legs following exercise recovery and a subsequent insulin treatment, quantifying 12,619 Class 1 phosphopeptides. Typically, inter-subject variation is considered a limitation of large-scale omics measurements. Our experimental design enabled repeated-measures analyses, facilitating the classification of >1,500 phosphopeptides regulated by exercise and/or insulin in the study. Moreover, we exploited the heterogeneity in subject responses to exercise and insulin treatment, to statistically identify phosphorylation sites associated with improved glucose uptake. In concert with the phosphoproteomics, we measured glucose uptake into the specific muscles that were biopsied in response to the hyperinsulinemic-euglycemic clamp. By measuring temporal changes in the phosphoproteome along with simultaneous subject-matched measures of muscle glucose uptake, we correlated signalling changes with muscle metabolism on an individual level. Insulin and exercise strongly potentiated the glucose uptake of certain subjects, while other subjects responded less effectively. Strikingly, we observed phosphosites that displayed identical heterogeneity among the subjects. Correlating phosphosites with glucose uptake across the individuals highlighted phosphosites on proteins known to be involved in glucose uptake, as well as potential novel players. This analysis also identified a kinase that has not previously been reported to promote insulin sensitivity as regulating a large proportion of these glucose uptake-associated phosphosites. By considering individual responses and linking these to glucose uptake, these data reveal a landscape of how exercise promotes insulin signalling, providing novel targets to therapeutically promote muscle insulin sensitivity.