The comparative effects of gamma irradiation an ozone treatment on the microbiological and physicochemical qualities were investigated for the improvement of hygienic quality of aloe powder and bee pollen. Gamma irradiation at 7.5~10kGy could reduce total aerobic bacteria, molds and coliforms below detection levels, but ozone treatment up to 18 ppm for 8hr was not sufficient to eliminate the microorganisms from aloe powder and bee pollen. The physicochemical properties such as fatty acid an amino acid compositions, mineral content, TBA value, barbaloin and pigment contents were not significantly changed by gamma irradiation, whereas ozone treatment caused significant changes in fatty acid composition, lipid oxidation and destruction of barbaloin and natural pigments.