Physical activity is associated with beneficial adaptations in metabolic health. We studied over 50 complex traits before and after exercise intervention in a panel of 100 diverse strains of female and male mice, known as the Exercise Hybrid Mouse Diversity Panel, ExcHMDP. Candidate gene analyses in three brain regions, muscle, liver, heart, and adipose tissue of animals revealed genetic drivers of clinically relevant traits including volitional exercise volume, adiposity, muscle metabolism, and hepatic lipids. Although ~33% of genes differentially expressed in skeletal muscle following the exercise intervention were similar between mice and humans independent of BMI, responsiveness of adipose tissue to exercise-induced weight loss appears strongly influenced by sex and underlying genotype. We identified ubiquitin-like protein modifier, Ubd1, as a top differentially expressed adipose tissue transcript in response to acute running, long-term exercise training intervention, and high fat diet feeding. We leveraged genetic diversity of the ExcHMDP to generate prediction models of metabolic trait responsiveness to volitional activity, and to enhance data mining and hypothesis development, we made the ExcHMDP data publicly available via user-friendly web-based application (https://exchmdpmg.medsch.ucla.edu/app/).