Rice (Oryza sativa L.) is a vital global staple, with aroma being a key factor in its market value. The compound 2-acetyl-1-pyrroline (2-AP) is the primary contributor to the fragrance of aromatic rice. However, storage conditions significantly impact the aromatic and nutritional quality of rice. This study evaluated the effects of temperature and duration on 2-AP retention, protein stability, and moisture content in Cambodia’s fragrant Phka Rumduol rice over 12 weeks. Samples were stored at 4°C, room temperature (RT), and 40°C, and analyzed using near-infrared spectroscopy for protein and moisture content and gas chromatography–mass spectrometry for 2-AP quantification. Results revealed a significant decline in 2-AP content, particularly at 40°C, where 2-AP levels decreased by 67.44%, compared to losses of 46.71% at 4°C and 52.46% at RT. High temperatures also caused protein denaturation and increased moisture volatilization, while cold storage at 4°C effectively preserved 2-AP levels by minimizing these losses. Although storing rice at RT resulted in moderate 2-AP degradation, it remains a feasible and cost-effective option with appropriate packaging. The study underscores the necessity of optimizing storage temperature and duration to preserve the aromatic and nutritional quality of fragrant rice. Future research should investigate advanced storage technologies, particularly enhanced packaging, to further reduce quality deterioration during post-harvest.