Soil acidification exerts detrimental effects on rice plant leading to severe reduction in its yield. In the present study, we investigated the physiological, biochemical and microstructural changes in the leaves of rice cultivars, namely, Jhilli Dhan (JD) and Gora Dhan (GD), under varying pH conditions (pH 6.5, 5.5, 4.5 and 3.5). Seedlings were grown at varying pH levels for 14 days under controlled conditions. Root and shoot growth and chlorophyll content were found to be decreased with increasing acidity, whereas electrolyte leakage was increased with increasing acidity. Overall, seedling growth was significantly reduced at pH 3.5, while, it was maximum at pH 6.5 treatment, which might be the result of cumulative altered physiological parameters. Further, biochemical parameters, namely total soluble sugar (TSS), proline content and lipid peroxidation were found to be positively correlated with acidity. Microstructural changes were observed through Swept-Source Optical Coherence Tomography (SS-OCT) and Field Emission Scanning Electron Microscope (FESEM). The thickness between different layers of leaves was found to be disintegrating at low pH conditions and the thickness of parenchyma cells was reduced significantly. FESEM analysis revealed changes in characteristics of stomata under acidic stress. The understanding of physiological, biochemical and microstructural changes in rice leaves under varying pH conditions may help in developing rice with improved tolerance towards soil acidity stress.