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Pumpkin Cookies Recipe FAQ Can you freeze pumpkin cookies? Yes, you can freeze pumpkin cookies. Store them in an airtight container in the freezer with parchment paper between the layers. What are pumpkin cookies? Pumpkin cookies are like a combination of pumpkin muffins and sugar cookies. Are pumpkin cookies healthy? Although pumpkin cookies do contain pumpkin puree, they are considered a dessert and can be enjoyed in moderation as part of a healthy diet.