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A stack of paleo pumpkin chocolate chip muffins on a white wood background near cinnamon sticks and chocolate chips

Paleo Pumpkin Chocolate Chip Muffins with Crumb Topping

These Paleo Pumpkin Chocolate Chip Muffins with Crumb Topping are grain-free, gluten-free, and delicious! Naturally sweetened, they make a great healthy treat and are perfect for fall and pumpkin season! The sweet and slightly crunchy paleo crumb topping compliments these muffins so well, the entire family will love them!
Course Breakast, Paleo Baked Good
Cuisine American
Prep Time 10 minutes
Cook Time 30 minutes
Total Time 40 minutes
Servings 12 Muffins
Calories 319kcal


  • 1 ½ cup blanched almond flour
  • ¼ cup tapioca flour
  • tsp pumpkin pie spice
  • tsp baking powder
  • ½ tsp salt
  • 1 cup pumpkin puree not pumpkin pie filling
  • 3 large eggs
  • cup coconut sugar
  • 1 tsp vanilla
  • 1 cup chocolate chips see notes

Paleo Crumb Topping

  • ¾ cup almond flour
  • ¾ cup pecans very finely chopped
  • 3 tbsp ghee solid, not melted
  • ¼ cup coconut sugar
  • 1 tsp pumpkin pie spice


  • In a large bowl mix the dry ingredients together; almond flour, tapioca flour, pumpkin pie spice, salt and baking powder.
  • In a separate bowl, whisk together the wet ingredients and the sugar; pumpkin puree, eggs, coconut sugar, and vanilla.
  • Add the wet ingredients to the dry ingredients and mix together well.
  • Fold in the chocolate chips and set aside the muffin batter while you make a crumble to allow the tapioca flour to absorb more liquid before baking.
  • In a small bowl add all ingredients for the crumble and using the back of a fork or a pastry cutter, mix ingredients to form a crumble.
  • Prepare the muffin pan with liners and give the muffin batter one final mix. Fill each muffin cup nearly all the way full, evenly dividing the batter between the 12 muffin liners.
  • Evenly divide the crumble between the 12 muffins and very gently press down into the batter.
  • Bake at 350F for 25 to 30 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
  • Allow the muffins to cool in the pan for 5 minutes and then gently remove them from the pan and transfer to a cooling rack. Let them cool completely before storing and enjoy!


  • Be sure you are using blanched almond flour and not almond meal.  Almond meal is simply ground almonds containing the skin. It is far more coarse than almond flour and will typically cause your baked goods to have a much different texture and be far more dense than almond flour.
  • I prefer to chop Hu Chocolate bars into chunks, or use Enjoy Life Foods mini chocolate chips and dark chocolate morsels to keep these paleo and dairy free.
  • These muffins are best stored in an airtight container in the fridge for up to 4 days. Store them with a paper towel to absorb any moisture and prevent them from becoming too moist while storing.
  • Unfortunately, most gluten free flours can NOT be substituted for one another on a one to one ratio. That being said, I never recommend substituting one gluten free flour for another in any recipe unless specifically stated that it has been tested.


Sodium: 197mg | Calcium: 94mg | Vitamin C: 1mg | Vitamin A: 3250IU | Sugar: 15g | Fiber: 4g | Potassium: 90mg | Cholesterol: 59mg | Calories: 319kcal | Trans Fat: 1g | Monounsaturated Fat: 4g | Polyunsaturated Fat: 2g | Saturated Fat: 6g | Fat: 23g | Protein: 7g | Carbohydrates: 27g | Iron: 2mg