Abstract: The chemically complex and diverse nature of the plant metabolome require several platform technologies to profile the entire range of metabolites. An ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) technique was used to profile and identify a set of small-molecule metabolites found in heat treated whole palm oil extract. An investigation was carried out on the effect of heat treatment on the yield, quality and metabolites profile for whole palm oil extract. Palm fruits were collected, cleaned and sterilized for 0, 20, 40 and 60 min. The pulps were then stripped from the sterilized fruits and later was pressed using laboratory scale expeller. The resulting puree was centrifuged at 4000 rpm for 20 min. The result shows that there was a significantly difference between sterilization time of 0 and 40 min in yield and quality. Of all, the highest oil yield of 19.9±0.21% (w/w) was obtained at 40 min of sterilization with DOBI value of 5.95±0.08 and FFA of 1.44±0.22%. The MarkerView software version 1.2.0.1 analysis of the UPLC-ESI-MS/MS preliminary experimental data demonstrated the distribution and identity of several compounds in the whole palm oil extract for 40 min sterilization and 0 min sterilization. This study have demonstrated the potential of UPLC-ESI-MS/MS to identify, characterize and profile the metabolites in heat treated whole palm oil extract for further research in developing health application of phytochemicals from palm oil.