Effect of storage duration on changes in the popping behaviour due to structural, physico-chemical, and crystalline properties alterations of raw, roasted and 6-month stored roasted makhana seeds was studied using scanning electron microscopy (SEM), FTIR, GC-MS. Dynamic light scattering (DSC), x-ray diffraction (XRD), and differential scanning calorimetry (DSC) analysis. The roasted seed were stored in under airtight polypropylene packets for 6 months. Popped makhana recovery did not change significantly up to 150 days of storage and decreased significantly thereafter. SEM analysis showed that the capillaries were formed in the roasted kernel after 6-months storage due to slow release of water molecules as a result of starch retrogradation during storage. FTIR analysis showed similar peaks for the functional groups and 16 volatile compounds were identified by GC-MS analysis. Hydrated particle size of the samples decreased after 6-month storage, which was less than popped makhana but higher than raw makhana seeds. Long chains of amylopectin broke into shorter double helices after storage. Degree of crystallinity of raw, fresh roasted, and 6-month stored roasted seeds were 31%, 22.5%, and 30%, respectively. Increase in crystallinity was found to be responsible for the significant reduction in popped makhana recovery after 6-months storage because the water molecules detached from the starch were trapped in the capillaries and changed the starch structure to the crystalline phase.