In Malaysia, core oil palm trunk (COPT) is one of the biomass that has been left underutilised due to its low properties. Nonetheless, metabolites contained in COPT sap may provide an alternative natural resources for bio-chemicals and pharmaceuticals. Metabolites such as sugars are easily affected by analytical factors during storage. In this study, the changes of metabolite contents in COPT sap stored at different storage durations, conditions and temperatures were observed by using gas chromatography-mass spectrometry (GC-MS) based metabolomics approach. The changes of metabolite contents, particularly sugars and organic acids were analysed using univariate and multivariate statistical analysis. The separation trends observed in the principal component analysis (PCA) score plot was greatly influenced by storage temperatures. However, two-way analysis of variance (ANOVA) revealed that the majority of significant metabolites (P<0.05) was strongly influenced by storage durations. The metabolite increased significantly when COPT was stored as raw rather than sap. The highest sugar concentrations in COPT were found at 10°C for one month (R-10-1M). Furthermore, the organic acids increased significantly when stored at 4°C for one month (R-4-1M). The results indicated different storage durations, conditions and temperatures led to variation in the COPT sap metabolite content.