Guggul is a gum oleo-resin, tapped from a data deficient plant- Commiphora wightii (Arnott.) Bhandari in India. It is extensively used in ayurvedic drugs and formulations since ages. Natural plant-based products; especially aromatic ones like guggul gum oleo-resin deteriorates, qualitatively during its storage and transits before reaching the industry for its value addition. This economical and ecological loss can be avoided if it is stored in proper containers. Physico-chemical degradation of guggul samples stored were analysed by scanned electron microscopy, fourier transformed infra red, thermogravimatric, Powdered X-ray diffraction and elemental analysis for carbon, hydrogen, nitrogen and sulphur. Physico-chemical degradation of guggul oleo-resin occurs with the age of storage and the type of storage containers used. Among the four storage containers (earthen pot, plastic jar, polythene bag, jute bag) evaluated, earthen pot was found to be the best in checking the qualitative loss of guggul even upto 24 months. The qualitative information generated in the study on guggul storage may be useful to the drug industry and guggul traders. It may encourage them practice storing guggul in earthen pots against current practice of using jute bags and polythene bags, to store it.