The study aimed to evaluate the effect of drying on the functional quality of stingless bee (Heterotrigona itama) honey. The honey was subjected to vacuum drying (40–60°C), vacuum evaporation (40–60°C), and freeze drying, respectively, to achieve a standardized moisture content. The dehydrated honey seemed to have a significant (p < .05) darker color (lower L* and higher b* values) as compared to the raw honey. Results suggested that the dryness of the dehydrated honey has significantly affected its antioxidant capacity except oxygen radical absorbance capacity (ORAC) assay. It seems vacuum drying at 60°C for 2.2 hr produced honey with higher total phenolic (300.24 ± 6.81 mg GAE/kg) and flavonoid contents (273.83 ± 2.52 mg QE/kg), which were also characterized by the highest 2,2‐azinobis‐(3‐ethylbenzothiazoline‐6‐sulphonate) (ABTS) (371.34 ± 2.57 µmol TE/100 g) and ferric reducing antioxidant power (FRAP) (344.20 ± 6.81 µmol Fe2+/100 g). Rosmarinic acid and quercetin are the most dominant phenolic compounds found in the dehydrated honey. In conclusion, vacuum drying could be an efficient way to improve honey physicochemical and functional stability. Practical applications Stingless bee honey production is a new emerging industry in tropical and subtropical countries. The keeping quality of stingless bee honey is limited due to its nature of high moisture content. Thus, removal of excessive moisture from the honey is necessary to maintain the product quality and stability particularly during handling and storage. The application of low‐pressure dehydration processes can aid the evaporation process of water from stingless bee honey. The findings of the present work provide a better insight toward the effect of low‐pressure dehydration on the physicochemical quality and functional properties of stingless bee honey in addition to extend its shelf life.