Physical inactivity affects multiple organ systems, including the musculoskeletal system, which upsets the delicate balance of several secretory factors leading to metabolic derailment. This reduces contractile recruitment of the skeletal muscle with dampening of its oxidative capacity resulting in impaired intramuscular lipid metabolism and substrate utilization. We hypothesized that this altered phenotype would also have an indispensable effect on circulatory cytokines and the level of metabolic intermediates. In this study, comparison between sedentary (SED) and exercised (EXER) animal models showed that organismal metabolic parameters (body mass, oxygen utilization and glucose tolerance) are altered based on physical activity. Our data suggest that cytokines linked to glycemic excursions (insulin, c-peptide, glucagon) and their passive regulators (leptin, BDNF, active ghrelin, and GIP) exhibit changes in the SED group. Furthermore, some of the proinflammatory cytokines and myokines were upregulated in SED. Interestingly, serum metabolite analysis showed that the levels of glucogenic amino acids (alanine, glycine, tryptophan, proline and valine), nitrogenous amino acids (ornithine, asparagine, and glutamine) and myogenic metabolites (taurine, creatine) were altered due to the level of physical activity. A pyrimidine nucleoside (uridine), lipid metabolite (glycerol) and ketone bodies (acetoacetate and acetate) were found to be altered in SED. A Spearman rank correlation study between SED and CTRL showed that cytokines build a deformed network with metabolites in SED, indicating significant modifications in amino acids, phosphatidylinositol phosphate and glycerophospholipid metabolic pathways. Overall, long-term physical inactivity reorganizes the profile of proinflammatory cytokines, glucose sensing hormones, and protein and glycerophospholipid metabolism, which might be the initial factors of metabolic diseases due to SED.