You can use spices to add flavor when you roast your pumpkin seeds such as salt, nutmeg, cayenne pepper, and even chili powder. Cool the pumpkin seeds before storing to avoid trapping moisture in the storage container. Pumpkin seeds will go rancid more quickly if exposed to moisture. Store in an airtight container. A hard plastic storage container or disposable storage container is ideal because it creates an airtight seal to keep them fresh. However, if you live in an arid climate, you can store your seeds in a plastic bag. Refrigerate or freeze your pumpkin seeds. Pumpkin seeds can turn rancid even after you roast them if left at room temperature. They will remain fresh for up to 2 months if refrigerated.