An experiment was conducted at National Bureau of Plant Genetic Resources, New Delhi to assess physiological and biochemical parameters to identify factors contributing to the loss of seed viability. Ultra-dried seeds of Cotton, Safflower and Groundnut stored at different MTS and ambient condition, viz. Cotton MTS 3.3%, Cotton Ambient 3.3%; Safflower MTS 6%, Safflower Ambient 3.8%; Girshell MTS, Gir Ambient 6.2% were used for present study. Result showed significant difference for all the physiological and biochemical traits as the seeds that were stored at MTS condition having high germination percentage, high vigour index, less moisture content, and lower Electrical conductivity (E.C.) and higher Dehydrogenase activity in comparison with seeds that were stored at Ambient condition. In SDS-PAGE profile of Cotton, Safflower and Groundnut some of the old bands were found to be missing at Ambient condition while some new bands were found to be appear in case of seeds that were stored at MTS condition. Deterioration was observed in seeds that were stored at Ambient condition. Whereas seeds that were stored at MTS condition were not deteriorated as much when compared to seeds that were stored at Ambient condition.