Spicy Paleo Pumpkin Muffins

You can substitute any hard winter squash or carrots for the pumpkin.

To grate the pumpkin, cut it into large pieces, scoop out the seeds, and grate the flesh on a box grater until you hit the skin. Alternatively, you can cut away the skin and grate in a food processor.

  • Prep time: 20 minutes
  • Cook time: 20 minutes
  • Yield: 12


  • 2 1/2 cups almond flour
  • 3/4 cup tapioca starch
  • 1 1/2 tablespoons coconut flour
  • 1 teaspoon baking soda
  • 1 1/2 teaspoons baking powder
  • 1/2 tablespoon smoked paprika
  • 1 teaspoon crushed chili flakes (I used chipotle chili flakes)
  • 1 1/2 teaspoons ground cumin
  • 1/2 teaspoon salt
  • 4 large eggs
  • 1/2 cup olive oil, melted ghee, or melted butter
  • 2 tablespoons honey
  • 1 tablespoon red wine vinegar
  • 1 packed cup grated raw sugar or pie pumpkin (avoid jack-o-lantern pumpkins)
  • 1/2 cup diced red bell pepper
  • 1/2 cup diced onion
  • 3/4 cups toasted pepitas or pumpkin seeds (divided)

Special equipment:


1 Preheat oven to 350F. Line a muffin tin with muffin papers

2 Sift together the dry ingredients: Sift together the almond flour, tapioca starch, coconut flour, baking soda, baking powder, spices, and salt. I like to sift at least twice with Paleo baked goods to make sure there are no clumps and everything is well-mixed.

Paleo Pumpkin Muffins

3 Mix together the wet ingredients: In a separate bowl, beat the eggs, then whisk in the oil, honey, and vinegar.

4 Pour the wet ingredients into the dry and mix gently until combined.

5 Gently stir in the grated pumpkin, bell pepper, onion, and 1/2 cup of pepitas. Save the rest of the pepitas for topping. Rest the batter for at least 10 minutes so that the flours can hydrate.

6 Fill each muffin wells up to the top. Top each muffin with a few of the remaining 1/4 cup of pepitas.

7 Bake for 18 to 20 minutes. When done, the muffins should look toasted around the edges, be dry on top, and a toothpick inserted in the middle will come out clean.

Paleo Pumpkin Muffins

8 Cool and serve (or store): Transfer the muffins to a cooling rack. Cool briefly before serving, or cool completely and store in an airtight container at room temperature for 3 days (or refrigerate for up to a week).

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  • BS

    We dont take eggds, could you suggest a substitute for it? Thank you!

    • Sabrina Modelle

      Hi BS. I haven’t tested this without eggs. Paleo baking relies on eggs for moisture, protein, and binding. If I was going to test this with an egg substitute, I would try flax eggs. If you do end up trying it, please let us know what you did and how it turned out!

  • SusanT

    I’d like to try these, but cannot have tapioca flour. I was wondering if I might use spelt flour instead.

    • Sabrina Modelle

      Hi Susan,
      Spelt is a whole grain, so it will not have the same properties as tapioca which is pure starch. You could substitute arrowroot with similar results. Other than that, anything that is a pure starch might also work (think cornstarch or potato starch).
      If it’s starch you can’t eat, I don’t know that there is any 1:1 substitute for this recipe.
      Good luck, and I’d love to know what you come up with.

  • Sandy S

    This is my kind of recipe. It sounds delicious! I really like pumpkins for their flavor and ‘fill me up’ quality. Love that it is flexible for when I want or need to switch out an ingredient or two.

    • Sabrina Modelle

      Thanks, Sandy! It really is flexible and totally filling. I was thinking I might even try a version with cauliflower this weekend :)

      • Sandy S

        Hey Sabrina! I will look for a post to find out how your idea of using cauliflower turns out. I should think the cumin flavor would work well with it. I plan to try the recipe (straight-up) this weekend. Will post how it turns out. Wondering about trying a curry version in the future! Elise got me into curry with her Mulligatawny soup (Fabulous!) and I find ways of using it quite often now. My current new thing to play with is aquafaba. Amazing how it opens up my GF diet. May see about using it with this recipe down the road. Cheers!