Stingless bee honey (SBH) is a local and natural bee product produced by domestic stingless bee honey pots. The physicochemical and bioactivity contents can affect the types and botanical origin of stingless bee honey. This study aims to compare the physiochemical profiles and bioactive compounds of Heterotrigona itama (H. itama) and Trigona laeviceps (T. laeviceps) including pH, electrical conductivity (EC), colour intensity, and antioxidant properties. We analysed the physicochemical properties (pH, colour and EC) of SBH in different methods. Further, we quantified the antioxidant activities using ABTS assay and DPPH (IC50) assay. These findings showed that the pH, EC, and colour intensity values of H. itama were higher than T. laeviceps whereas the total phenolic content (TPC), total flavonoids content (TFC), IC50 and ABTS assay values of T. laeviceps were higher than H. itama. The empirical findings in this study provide new light and strong evidence supporting the potential use of SBH as an alternative therapeutic potential as pharmacological use.