Honey has been widely used for medicinal purposes since ancient times. It is produced by stinging bees or stingless bees by processing the collected nectar or plant sap in their bodies into raw honey. Extraction of honey will result in the pooling of crude volatile bioactive materials that could enhance its benefits. This work aims to compare the phytochemical characteristics of raw and methanol-extracted honeys in the Kelulut, Tualang and Manuka honeys. All types of raw honey samples were extracted by using the methanol extraction method and both groups were analysed using gas chromatography/mass spectrometry (GC/MS) at the National Poison Centre, Universiti Sains Malaysia, Malaysia. The findings showed that 23 compounds were identified in raw Kelulut honey and 18 compounds in methanol-extracted Kelulut honey; 28 compounds were identified in raw Tualang honey and 29 compounds in methanol-extracted Tualang honey; 19 compounds in raw Manuka honey and 22 compounds in methanol-extracted Manuka honey. There were differences in the phytochemical substances detected in raw and methanol-extracted honeys. The major compounds in raw honeys were mostly from the ketone, alcohol, and ester groups, whereas the ketone group was dominant in methanol-extracted honeys. Most bioactive substances identified in the methanol-extracted variant of honeys were more concentrated than the raw variant. A majority of these substances have antimicrobial characteristics.