These pumpkin muffins are made with dark chocolate, coconut oil, chia seeds and of course, pumpkin puree. Substitute walnuts for the chocolate if desired.Pumpkin and chocolate are such strange bedfellows, don’t you think? But they really are meant for each other and these Healthy Pumpkin Chocolate Chip Muffins are love at first bite. After several attempts to add healthy ingredients to this recipe, I think I have a winner.

I bumped up the antioxidants in the chocolate by using dark chocolate chips and used a mixture of whole-wheat flour and almond flour, switched out vegetable oil with coconut oil (you don’t need much because the pumpkin already makes these muffins moist) and added a few chia seeds to compliment the super good-for-you properties of the pumpkin. I reduced the sugar significantly, but you won’t miss it thanks to the sweet pumpkin puree, chocolate chips and coconut oil. Almond flour also has a nutty-sweet flavor so all in all, the sweetness of these muffins is just right. Chia seeds are purely optional and some people might be confused by the tiny popping crunchiness they add to the muffins, but we really like them.

These pumpkin muffins are made with dark chocolate, coconut oil, chia seeds and of course, pumpkin puree. Substitute walnuts for the chocolate if desired.Healthy Pumpkin Chocolate Chip Muffins mix up quickly by hand in one bowl, plus bake up moist and delicious. AND they just get better as they sit. In fact, I would plan on making them a day ahead if you can. (Photo note: The muffin that’s cut in the picture is super, super moist and was cut while still warm. As the muffins cool, they will achieve a more cake/muffin-like texture and appear less wet but still moist for up to three days.)

These pumpkin muffins are made with dark chocolate, coconut oil, chia seeds and of course, pumpkin puree. Substitute walnuts for the chocolate if desired.The pumpkin muffins are excellent with or without the chocolate if you’re not a fan of the two flavors together. The muffins are also incredible with chopped walnuts rather than the chocolate chips.

Healthy Pumpkin Chocolate Chip Muffins
Prep time
Cook time
Total time
These muffins are healthier than most with the addition of coconut oil, almond flour and dark chocolate. Quick and easy, and even better after they sit overnight. Try to make them a day ahead of time for an ultimate wow factor!
Recipe type: Sweets
Serves: 12-15
  • ¾ cup almond flour
  • ¾ cup plus 1 tablespoon whole wheat flour
  • 1 teaspoon pumpkin pie spice
  • 1 teaspoon ground cinnamon
  • 1 Tablespoon chia seeds (optional) plus extra for sprinkling on top
  • ½ teaspoon baking soda
  • 1 teaspoon baking powder
  • 1⅓ cup pumpkin puree
  • 2 Tablespoons coconut oil, melted
  • ⅔ cup firm-packed light brown sugar
  • 2 eggs
  • ½ teaspoon pure vanilla extract
  • ½ cup dark chocolate chips, rough chopped to distribute more throughout the batter
  • Optional: Chocolate chips can be replaced with walnuts or even oatmeal (not instant or quick cooking)
  1. Position oven rack in middle of oven and preheat oven to 350 degrees F. Line muffin tin(s) with cupcake liners. This batch makes 12 full muffins as shown in photos or 15 muffins level with the liners.
  2. In a medium bowl, combine pumpkin puree, coconut oil, brown sugar, eggs and vanilla extract. In the same bowl, sprinkle the flours, pumpkin pie spice, cinnamon, and chia seeds if using over the wet ingredients, and then sprinkle the baking soda and baking powder evenly over everything. Stir until well incorporated and the flours are well mixed in (Note: whole wheat flour can be stirred much more than all-purpose flour without creating a tough finished texture and since the almond flour is gluten-free, it can be stirred in even more with successful results).
  3. Now add your chocolate chips and give the mixture one last good stir.
  4. Fill muffin cups between ½ to ¾ full, depending on the size muffins you want. I filled mine ¾ full. They don't rise a lot, so if you want really big muffins, fill even more. Sprinkle with more chia seeds if you like.
  5. Bake for 23-25 minutes, until a toothpick inserted in the center comes out clean and tops begin to dry at the peaks. Place tin on cooling rack and cool completely.
  6. For even better muffins, remove from tins when cooled and place in air-tight container for 24 hours before serving.

Recipe loosely adapted from Joy of Baking.

Pumpkin Muffins made with whole-wheat and almond flour, coconut oil, dark chocolate and of course, pumpkin puree. Moist and tasty, mix in one bowl start to finish in under 30 minutes.

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