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The health benefits of the <i>Aquilaria crassna</i> Pierre ex Lecomte leaf extract (AE) make it very useful as an ingredient in food and pharmaceutical products. Iriflophenone 3,5-<i>C</i>-<i>β</i>-<span style="font-variant: small-caps;">d</span>-diglucoside (<b>1</b>), iriflophenone 3-<i>C</i>-<i>β</i>-<span style="font-variant: small-caps;">d</span>-glucoside (<b>2</b>) and mangiferin (<b>3</b>) are bioactive compounds of AE. We assessed the stability of AE by investigating the thermal degradation kinetics and shelf-life (<i>t</i>_90%) of compounds <b>1</b>, <b>2</b> and <b>3</b> using Arrhenius plot models and studied their pH-rate profiles. The results demonstrate that <b>1</b> and <b>2</b> were degraded, following a first-order kinetic reaction. The degradation of <b>3</b> followed first-order reaction kinetics when present in a solution and second-order reaction kinetics in the dried powder form of the extract. According to the first-order kinetic model, the predicted shelf-life (<i>t</i>_90%) of the extract at 25 °C in dried form for compound <b>1</b> was 989 days with activation energy 129.86 kJ·mol⁻¹, and for <b>2</b> it was 248 days with activation energy 110.57 kJ·mol⁻¹, while in the extract solution, the predicted shelf-life of compounds <b>1</b>–<b>3</b> was 189, 13 and 75 days with activation energies 86.83, 51.49 and 65.28 kJ·mol⁻¹, respectively. In addition, the pH-rate profiles of <b>1</b>–<b>3</b> indicated that they were stable in neutral to acidic environments.