Spicy Paleo Pumpkin Muffins

Photography Credit: Sabrina Modelle

Pumpkin pancakes and cinnamon rolls are well and good, but what about those of us who like something savory instead of sweet for our weekday breakfasts? These Paleo muffins prove that pumpkin plays just as well with cumin and paprika as it does with cinnamon and nutmeg.

These muffins make a great grab-and-go breakfast or a healthy afternoon snack. They are also grain-free and very nutritious!

I used a small pie pumpkin in these muffins, though you could use any hard winter squash or carrots. Just avoid pumpkin puree because the muffins will end up too wet. (Also avoid the giant pumpkins used for carving jack-o-lanterns; those aren’t very tasty!)

If Paleo baking feels daunting, this is a great recipe to start with. You only need a few special paleo flours and the recipe is really easy to mix together. Be sure to let the batter rest for a few minutes before baking the muffins to give the flour time to absorb the moisture.

Paleo Pumpkin Muffins

Here’s a brief run down of the flours we’ll be using in this mix:

Ground Almond Flour: Ground almond flour is made from blanched almonds with the skins removed. Look specifically for “fine ground” flour for this recipe. This is key for muffins with a light texture. Coarse almond flour will be heavier and have a tendency to clump.

Almond flour a great base flour for Paleo baking because it has a very neutral flavor. It also gives baked goods a tender crumb and it has pretty good binding power (something non-gluten flours are often missing). Because of the high fat content of almond flour, we don’t need as much other fat in the recipe.

Coconut Flour: Coconut flour is made from the fibers of ground coconut. It will absorb up a TON of moisture in recipes, so it’s usually used in conjunction with other flours. Coconut flour tastes mildly of coconut, but because we’re using just a small amount, it won’t add a lot of flavor to this recipe.

Tapioca Flour : Tapioca flour, also known as tapioca starch, is the pure starch of the cassava. It has very good binding power and also lightens up a batter made with the almond and coconut flours. It is neutral in taste.

Paleo Pumpkin MuffinsYou can find all these flours at natural food stores, like Whole Foods. Many nationwide grocery stores are also starting to stock them more regularly. Look in both the baking aisle and the bulk bin section.

The muffins are also very forgiving to first-time Paleo bakers and quite versatile. I’ve made them with carrots instead of pumpkin and even added a 1/2 cup of crumbled feta into the batter – both versions turned out great. You could even add in some cooked sausage or crumbled bacon for extra protein!

The muffins are moist, flavorful, and keep well. We stored them covered at room temperature for a couple of days. For longer storage, wrap tightly and refrigerate.

Spicy Paleo Pumpkin Muffins Recipe

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

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.


  • 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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Sabrina Modelle

Sabrina Modelle started The Tomato Tart in 2010. Since then, recipes and photographs have been featured in media outlets, worldwide. The site features handmade, homemade, food that happens to be gluten free. When she’s not working, Sabrina can be found with her nose in a cookbook and a dog in her lap.

More from Sabrina

Paleo Pumpkin Muffins


  1. 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!

  2. 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.

  3. 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!

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