Organic soil amendments attract considerable attention, given their potential to promote nutrient recycling and contribute to reducing CO2 emissions. To evaluate their effects on quality characteristics of agricultural products, we comprehensively analyzed the metabolite compositions of radish (Raphanus sativus L.) leaves and roots using gas chromatography mass spectrometry (GC/MS). A field experiment arranged in a split-plot design investigated the effect of three levels of composted dairy manure amendments (0, 2 and 4 kg m−2; main plot) factorially combined with three levels of inorganic nitrogen (N) fertilization (0, 6 and 12 g N m−2 as ammonium sulfate; subplots) on radish metabolites. For both leaf and root metabolites, a principal component analysis was applied to all 124 metabolite peaks revealed by the GC/MS analysis. The first principal component accounted for 46.3% of the total variance and indicated a close relationship between metabolite profiles and inorganic-N (Ninorg) application rates, whereas the second principal component, accounting for 14.6% of the total variance, pointed to a close relationship between the metabolite profiles and the manure application rates. Leaf metabolites were more sensitive to inorganic-N and manure rates than root metabolites. Amino acids in roots and leaves showed a close relationship with Ninorg application rates, whereas the response to the level of manure was not clear. Organic acids in leaves were closely related to both Ninorg and manure levels. With increased amounts of applied manure, the concentrations of malic acid, myo-inositol-phosphate and sucrose decreased, whereas the concentrations of shikimic acid, arabinose and L-methionine increased. The observation that radish metabolites clearly differed under different application rates of both Ninorg and manure will prove useful in improving and distinguishing the quality of agricultural products grown using organic fertilizers.