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pumpkin chocolate chip muffins on a plate

Paleo Pumpkin Chocolate Chip Muffins

These gluten-free pumpkin muffins are adapted from The Essential Thyroid Cookbook. They are a great recipe for fall, but pumpkin’s nutrition profile makes them perfectly fine to enjoy year-round. If you can’t do the chocolate chips, chopped apples would make them equally delicious.
Prep Time 10 minutes
Cook Time 25 minutes
Total Time 35 minutes
Servings 12 muffins



  1. Preheat oven to 375°F. Line a muffin tin with paper muffin cups liners.
  2. Mix dry ingredients (flour, sugar, flaxseeds, baking soda, cinnamon, and salt) together in a large bowl with a whisk or a fork. Ensure that any lumps in the flour are broken up.
  3. In a separate bowl, whisk eggs, pumpkin puree, maple syrup or honey, and vanilla together until well combined.
  4. Combine the wet and dry mixtures and stir with a rubber spatula until well mixed. Gently fold in chocolate chips, taking care to avoid over-mixing. Batter will be thicker than most muffin batters, but will be spoonable.
  5. Spoon batter into muffin cups until approximately ¾ full. Place muffin tin in the oven and bake for 20-22 minutes, until tops are golden. Test doneness by inserting a toothpick into the center of a muffin. If it comes out clean, the muffins are done.

Recipe Notes

Cook’s notes: Maple sugar, Sucanat, or any other unrefined granulated sweeteners can be substituted for coconut sugar. Paleo adaptation: Omit dark chocolate chips if concerned about small amount of cane sugar.