To medically use and store proteins like enzymes, long-term maintenance of their activity must be considered. We examined the effectiveness of several methods for preserving the activity of three model-protein solutions. Solutions of catalase, L-lactate dehydrogenase, and carbonic anhydrase were used to form gas hydrates with xenon and natural gas. These enzyme aqueous solutions showed inhibitory effects on hydrate formation, and exhibited significant differences in induction time as well. The hydrates formed of enzyme solutions with xenon or natural gas are expected to have a better preservation effect than storage at room temperature and in liquid nitrogen. Changes in the activity of enzymes stored under different conditions were measured in relation to storage time. Storage in hydrate was good for maintaining the activity of catalase and L-lactate dehydrogenase. For carbonic anhydrase, the activity at room temperature was generally similar to that after storage in gas hydrate, but storing it in liquid nitrogen produced better results. For certain enzymes, storage in gas hydrates is expected to be a more effective method of maintaining activity than protein storage methods like freeze-drying, which causes mechanical damage to the protein.