The aim of our study was to investigate the relationship between objectively measured physical activity (PA) and cardiorespiratory fitness (CRF) and serum metabolites measured by targeted metabolomics in a population- based study. A total of 100 subjects provided 2 fasting blood samples and engaged in a CRF and PA measurement at 2 visits 4 months apart. CRF was estimated from a step test, whereas physical activity energy expenditure (PAEE), time spent sedentary and time spend in vigorous activity were measured by a combined heart rate and movement sensor for a total of 8 days. Serum metabolite concentrations were determined by flow injection analysis tandem mass spectrometry (FIA-MS/MS). Linear mixed models were applied with multivariable adjustment and p-values were corrected for multiple testing. Furthermore, we explored the associations between CRF, PA and two metabolite factors that have previously been linked to risk of Type 2 diabetes. CRF was associated with two phosphatidylcholine clusters independently of all other exposures. Lysophosphatidylcholine C14:0 and methionine were significantly negatively associated with PAEE and sedentary time. CRF was positively associated with the Type 2 diabetes protective factor. Vigorous activity was positively associated with the Type 2 diabetes risk factor in the mutually adjusted model. Our results suggest that CRF and PA are associated with serum metabolites, especially CRF with phosphatidylcholines and with the Type 2 diabetes protective factor. PAEE and sedentary time were associated with methionine. The identified metabolites could be potential mediators of the protective effects of CRF and PA on chronic disease risk.