Healthy Paleo Pumpkin Muffins

By Jess

5 from 1 ratings

Who says you can’t have baked goodies on a Paleo diet?! Not me! Look, let’s be honest: if I couldn’t occasionally have something bread-like, I don’t know if I could make it. There’s just some times in life that call for muffins. And when I hear that call, these pumpkin muffins with homemade pumpkin puree are one of my go-tos.


Trust me on this: These pumpkin muffins with homemade pumpkin puree are perfect for a brunch gathering or breakfast with a group.

Pumpkin makes a lot of people think “fall.” But I love pumpkin year round. Of course, if you want to use a big ole actual pumpkin, you may have to wait until fall to make this recipe. Pumpkin is in the squash family and squashes generally aren’t ready until very late summer, and into the fall. But, even though there are few times you’ll hear me say this, you can also use canned pumpkin puree for this recipe. And that, of course, you can get year-round.

Most muffin recipes rely on wheat flour but since us Paleo folks don’t eat wheat flour in this recipe we use almond and coconut flours, which are perfectly Paleo-friendly. A mix of both the almond and coconut flours helps with the texture of these muffins, so do use both.


The sweetness in the muffins comes from our favorite all-natural sugar: honey. Again, we love honey on the Paleo diet. And if you’re wondering about the apple cider vinegar, it helps the dough form a fluffy, cake-like texture in the muffin.

pumpkin muffin ingredients

If you’ve been following me for a while, you probably know what ghee is, but in case you’re new to the Paleo lifestyle, let me explain. Ghee is a type of clarified butter. To make ghee at home, heat butter in a pan over medium heat. When it melts and then begins to boil, there will be a foam on top, which at some point will cook off – it’s basically water.

When a new foam starts to appear, your ghee is ready. Pour it into a heat-safe container, leaving any brown bits on the bottom of the pan in the pan and, once it’s cool, put a tight lid on it to keep it safe from moisture. That’s ghee!

I like to just buy my own high quality, organic ghee. It can be such a hassle to make and I use it all the time!

homemade pumpkin muffins

These muffins just taste great. You get the savory pumpkin, the simply sweet honey, and one of my favorite spices – cinnamon – to top it all off. Of course the pumpkin serves an additional purpose in this recipe, other than taste: it keeps the muffins deliciously moist and tender. And the walnuts on top give each bite a delicious little chewy-crunchy extra something.

muffin recipe

While I would love to have these muffins every morning, I usually make them when I’m having guests. After all, it’s hard for me to get through 12 whole muffins, eating one a day, before the last few get a bit stale (although keeping them in an airtight container will help with that). So whenever I’m having guests over the weekend or friends over for brunch, I definitely add these pumpkin muffins with homemade pumpkin puree to the menu.

And the best part is that they will make both your Paleo and non-Paleo friends happy!


    • 1 ¼ pound baking pumpkin, seeds removed and sliced or ¾ cup canned pumpkin puree
    • 1 cup almond flour
    • ½ cup coconut flour
    • ½ tsp baking soda
    • 1 tsp apple cider vinegar
    • 2 ½ tsp ground cinnamon
    • 3 tbsp melted ghee
    • 3 eggs
    • ¼ cup honey
    • ¼ cup chopped walnuts


  1. Preheat oven to 350°F. Place the pumpkin slices in a baking dish,
  2. sprinkle with a pinch of cinnamon and bake for 40-45 minutes or until pumpkin is fork-tender.
  3. Remove from the oven and let cool slightly. Remove the pumpkin skin.
  4. Using an immersion blender or food processor, puree the pumpkin meat.
  5. Take ¾ cup pumpkin puree and set aside. If there's any leftover
  6. pumpkin puree, freeze it for another use.
  7. In a bowl combine the eggs with honey. Add the pumpkin puree, ghee, ground cinnamon and mix well.
  8. Add the almond flour, coconut flour and baking soda and mix
  9. to combine. Add vinegar and mix well.
  10. Line a 12-cup muffin pan with paper cups. Spoon the batter into the paper liners and sprinkle the chopped walnuts on top.
  11. Bake in preheated oven at 350 F for 20-25 minutes or until a toothpick inserted in the center comes out clean.
  12. Allow the muffins to cool on a rack, and enjoy!


Serving Size





Prep Time

15 minutes

Cook Time

60 minutes

Print Recipe

More Good Paleo-friendly Pumpkin Muffins

Healthy Pumpkin Streusel Muffins

Perfect for the fall, these pumpkin streusel muffins are packed with delicious flavors. Your taste buds will thank you for this incredibly tasty treat. A simple sweet and nutty crumble is prepared separately from the muffins and then sprinkled over the top before baking. The muffins can be stored in the refrigerator for up to three days.

Healthy Pumpkin Streusel Muffins Recipe


1 cup pumpkin puree
4 eggs
1/3 cup maple syrup
1/4 cup coconut oil, melted
1 cup almond flour
1/3 cup coconut flour
1 tsp cinnamon
1/2 tsp ground ginger
1/2 tsp salt
1/2 tsp baking soda
Pinch of nutmeg
Pinch of ground cloves

For the streusel:

1/2 cup almond flour
2 tbsp coconut oil, melted
2 tbsp maple syrup
1/2 tsp cinnamon
1/4 tsp salt
3/4 cup walnuts, finely chopped


1. Preheat the oven to 325 degrees F. Line a muffin tin with cups. In a small bowl, stir together the ingredients for the streusel and set aside.

2. In a separate bowl mix together the pumpkin, eggs, maple syrup, and coconut oil with a hand blender. Add the almond flour, coconut flour, cinnamon, ginger, salt, baking soda, and nutmeg. Blend to combine.

3. Divide the batter equally among the muffin cups, filling each cup about 3/4 of the way full. Sprinkle the streusel topping evenly over the muffins. Bake for 25-30 minutes, or until a toothpick inserted into the center comes out clean. Let cool for 5 minutes in the pan, then transfer to a wire rack to cool completely.


Ask a Question 

  1. Coconut oil, sugar and flour cause me to reflux. Even though they’re not paleo could i substitute brown rice flour, buckwheat, tapioca oatmeal flour etcetera for the coconut flour? I know coconut flour has a different absorption and expansion rate than most other flours. Which flour in your experience which flour substitutes closest to coconut flour

    • Hi Barbie,
      Sure, you can substitute coconut flour with others flours but I can’t tell you how much other flour do you need, because I didn’t test it. If you try, please let me know how it turns out.

  2. Thanks for doing a recipe that actually makes 12 muffins. I get frustrated when I see recipes for 8 or 9 muffins. Muffin pans come in dozens, or half-dozens. Will likely try this one!

  3. This is the first paleo muffin recipe that I have really loved! It makes such a nice light texture…not so heavy as others, perhaps due to the vinegar/baking soda reaction? Anyway, thank you…and I’m stoke because my kids love these too! It makes giving them a treat a lot easier when I find recipes like this! 🙂

    Rating: 5
  4. Just made these, flavours good but I would definately leave out the coconut flour next time.. it makes them too dry.. the ground almonds are sufficient enough as a binder.

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