Trehalulose, a rare disaccharide absent in Apis mellifera honey, has emerged as a distinctive biochemical marker of Indonesian stingless bee honey; however, its stability and consistency under processing and storage conditions remain underexplored. In this study, raw and dehumidified stingless bee honey (Trigona sp.) were analyzed using HPLC-RID to quantify trehalulose and evaluate quality parameters including color, acidity, and moisture after storage at − 20 °C, 4 °C, 25 °C, and 35 °C for eight weeks. Trehalulose concentrations varied geographically (0.00–40.22 g/100 g) but were generally present across most regions, confirming its diagnostic value as a qualitative authenticity marker. Dehumidification increased trehalulose levels from 40.22 to 47.56 g/100 g by reducing moisture below 20%. During storage, trehalulose decreased more rapidly in raw honey (40% to 29% at 35 °C) than in dehumidified samples (49% to 38%). Although high-temperature storage darkened honey due to Maillard reactions, dehumidification combined with cold storage most effectively preserved trehalulose, controlled acidity, and extended product stability. © The Author(s) 2026.