The bee products including honey, propolis, pollen, and bee venom have been reported to have therapeutic benefits in traditional and conventional medicine. Honey is collected from nectar which appeared as caramelised sugar, while propolis is mainly composed of plant resins and exudates that bees gather. Many studies demonstrated anti-inflammatory, anti-bacterial, anti-oxidant and anti-proliferative properties of honey and propolis extract.However the chemical profiling of Malaysian honey and propolis has not been well studied. The composition of honey and propolis depends on its geographical origin and also on its botanical source. Furthermore, the extraction of secondary metabolites from propolis is very crucial because its bioavailability is only 2% in raw form. Metabolomics tools have been applied employing liquid chromatography-high resolution mass spectrometry (LC-HRMS) and nuclear magnetic resonance (NMR) to afford an intensive chemical profile of the propolis samples to target the bioactive metabolites.The obtained HRLCMS data was processed with MZmine 2.10 and was dereplicated using an in-house Excel Macro to couple the MS data with the Dictionary of Natural Products 2016 database. A supervised multivariate analysis was done by orthogonal partial least squares discriminant analysis (OPLS-DA) in SIMCA-P 14.0 to predict and pinpoint the plausible bioactive components against respective cancer cell lines. The chemical profiling of honey from Malaysia and New Zealand were also obtained using the same metabolomics approach.However, isolation work was only done for propolis due to their potent bioactivities. Ten compounds have been isolated from Malaysia and New Zealand propolis, which consisted mainly of triterpenoid and flavonoid derivatives, respectively. Several compounds revealed anticancer properties on several cancer cell lines (lung, breast and ovary), as well as phenotypic alteration on zebrafish embryo that can be related with activation of Notch signalling for anticancer study.