Physical activity (PA) has been shown to associate with many health benefits but studies with metabolome-wide associations with PA are still lacking. Metabolome studies may deepen the mechanistic understanding of PA on the metabolic pathways related to health outcomes. The aim of the present study was to study the association of accelerometer based sedentary time (SB) and PA with metabolome measures. SB and PA were measured by a hip-worn accelerometer in 314 young adult men (age: mean 28, standard deviation 7 years). Metabolome was analyzed from fasting serum samples consisting of 66 metabolome measures (nuclear magnetic resonance-based metabolomics). The associations were analyzed using a single and compositional approach with regression analysis. The compositional analysis revealed that 4 metabolome variables were significantly (γ: 0.32–0.44, p ≤ 0.002), and 13 variables with a trend towards significance (p < 0.05), associated with SB with varying metabolic pathways. Trends towards significant associations (p < 0.05) were observed with 5 variables with moderate-to-vigorous and 1 variable with light intensity PA with varying metabolic pathways. The present study revealed possible mechanistic pathways relevant for the interaction between especially SB but also PA of moderate-to-vigorous intensity with ketone bodies and amino acid concentration related to exercised-induced energy production and lipid metabolism.