• The timescale of obesity-related knee osteoarthritis pathogenesis is slower than systemic metabolic and functional changes. • A high-fat diet and voluntary wheel running altered osteophyte formation, subchondral tibial bone mineral density, and relative tibial trabecular bone volume prior to diet or activity-induced changes in cartilage damage. • "Pre-osteoarthritis" high-fat diet and exercise-dependent phenotypes were explored using correlation network analyses to examine associations between systemic factors (i.e., metabolic, inflammatory, and biomechanical outcomes) and local knee structural changes during early-stage osteoarthritis. • Systemic and local knee structural outcomes in diet-induced obese mice were more strongly associated with circadian-related running patterns rather than running distance. • Sedentary and exercise networks were nearly completely distinct, suggesting that the biological relationships among systemic and local osteoarthritis-related variables are substantially altered the level of physical activity. Obesity increases knee osteoarthritis (OA) risk through metabolic, inflammatory, and biomechanical factors, but how these systemic and local mediators interact to drive OA pathology is not well understood. We tested the effect of voluntary running exercise after chronic diet-induced obesity on knee OA-related cartilage and bone pathology in mice. We then used a correlation-based network analysis to identify systemic and local factors associated with early-stage knee OA phenotypes among the different diet and exercise groups. Male C57BL/6J mice were fed a defined control (10% kcal fat) or high fat (HF) (60% kcal fat) diet from 6 to 37 weeks of age. At 25 weeks, one-half of the mice from each diet group were housed in cages with running wheels for the remainder of the study. Histology, micro computed tomography, and magnetic resonance imaging were used to evaluate changes in joint tissue structure and OA pathology. These local variables were then compared to systemic metabolic (body mass, body fat, and glucose tolerance), inflammatory (serum adipokines and inflammatory mediators), and functional (mechanical tactile sensitivity and grip strength) outcomes using a correlation-based network analysis. Diet and exercise effects were evaluated by two-way analysis of variance. An HF diet increased the infrapatellar fat pad size and posterior joint osteophytes, and wheel running primarily altered the subchondral cortical and trabecular bone. Neither HF diet nor exercise altered average knee cartilage OA scores compared to control groups. However, the coefficient of variation was ≥25% for many outcomes, and some mice in both diet groups developed moderate OA (≥33% maximum score). This supported using correlation-based network analyses to identify systemic and local factors associated with early-stage knee OA phenotypes. In wheel-running cohorts, an HF diet reduced the network size compared to the control diet group despite similar running distances, suggesting that diet-induced obesity dampens the effects of exercise on systemic and local OA-related factors. Each of the 4 diet and activity groups showed mostly unique networks of local and systemic factors correlated with early-stage knee OA. Despite minimal group-level effects of chronic diet-induced obesity and voluntary wheel running on knee OA pathology under the current test durations, diet and exercise substantially altered the relationships among systemic and local variables associated with early-stage knee OA. These results suggest that distinct pre-OA phenotypes may exist prior to the development of disease. Image, graphical abstract [ABSTRACT FROM AUTHOR]