Background: Ajwain is used as an antioxidant, as preservative and also valued for its medicinal properties. Ajwain seeds undergo deterioration during storage due to various microorganisms and leads to degradation of quality in terms of discolorations and altering the biochemical constituents. Hence, the effect of different types of storage conditions on quality of ajwain seeds was investigated. Methods: To assess the effect of storage in four different types of containers viz. Plastic jars (PJ) of make Pearl Pet, tin containers (TC), gunny bags (GB) and plastic lined gunny bags (PLBG) were used. The duration of storage was one year. External environmental conditions, i.e. temperature and relative humidity were recorded quarterly. To study the effect of different storage conditions on quality: (i) Seed quality assessment according to Agmark grade specifications (ii) incidence of mycoflora and (iii) effect on biochemical constituents viz. moisture, crude protein, crude fat, crude fiber, ash, carbohydrates, total soluble sugars, iron, total phenols and volatile oil contents were studied. Initial readings served as control for the experiment. Results: Irrespective of storage conditions, a sharp increase in deterioration was noted in stored samples of ajwain with respect to presence of shrivelled, damaged, discolored and weevilled seeds after 3 months of storage. This shifted the samples from good to substandard grade. Maximum deterioration was noted after 12 months. The incidence of mycoflora was found maximum in samples stored in tin containers and gunny bags followed by plastic lined gunny bags and plastic Jars. A decline in moisture, crude fiber, carbohydrates, total soluble sugars, iron and volatile oil contents and an increase in crude fat and ash contents were observed after 12 months of storage, irrespective of storage containers. Plastic jars were found to be the best of all containers studied for storage purpose.