The effect of oligochitosan O-80 treatment on metabolic changes in white radish (Raphanus sativus L.) sprouts (WRS) was investigated for its potential to enhance bioactive compounds accumulation. The seeds were germinated in deionized water containing different concentrations of oligochitosan O-80 (0 (control), 5, 10, 20 and 40 ppm). Seven-day old sprouts were harvested for metabolome analysis using liquid chromatography-mass spectrometry (LC-MS) and high-performance liquid chromatography (HPLC) for phenolic compounds and glucosinolate analysis, respectively, and spectrophotometric assays to determine the total phenolic content and antioxidant capacity. Partial least squares discriminant analysis was adopted to model the data from the LC-MS and revealed that O-80 at all tested concentrations affected the metabolite profiles of the treated WRS samples. The UV chromatogram at 320 nm showed increased levels of most sinapoyl derivatives, consistent with the increased total phenolic contents. Interestingly, glucoraphasatin (4-methylthio-3-butenyl glucosinolate), a major glucosinolate detected by HPLC, was increased by 40% in the sprouts treated with 10 ppm O-80. Our results provide compelling evidence regarding the exogenous application of oligochitosan O-80 as an elicitor of bioactive metabolites in WRS.