How to Make Healthy Pumpkin Chocolate Chip Muffins

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Pumpkin chocolate chip muffins are a tasty and healthy snack to keep on hand. If you love pumpkin spice everything then you will love these pumpkin chocolate muffins.

Made with clean simple ingredients and pure pumpkin puree these delicious muffins have a cake like texture and naturally sweet flavor.

These are part of our best healthy muffin recipes collection and one of our favorites too.

gluten free pumpkin chocolate muffins healthy

We love to keep healthy muffins in the house for snacking when someone wants a little treat. These healthier pumpkin chocolate chip muffins are light and moist and have a cake-like texture. They aren’t dense or overly sweet, making them a great option for an afternoon snack.

What You Need to make Healthy Pumpkin Chocolate Chip Muffins

To make these healthy pumpkin chocolate muffins you will need a few simple ingredients. Most of these ingredients are available at the local grocery store, or online.

  • 1/4 cup coconut flour
  • 1 tsp baking soda
  • 4 tsp pumpkin pie spice
  • 1/4 tsp salt
  • 4 eggs, room temperature
  • 1/4 cup coconut oil, melted
  • 1 cup pure pumpkin puree
  • 1/2 cup maple syrup
  • 1/2 cup dark chocolate chips plus 2 tbsp for muffins tops
  • 1 tsp vanilla bean powder

Ingredients Notes:

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For gluten free baking I often use almond flour. But coconut flour is another great option. Coconut flour is dense and you can use a lot less of it in baking recipes. You can get coconut flour online, as well as pure maple syrup.

When making anything pumpkin, you almost always need pumpkin pie spice. It is a combination of cloves, cinnamon, ginger and nutmeg, and it adds the perfect pumpkin flavor to your recipe. Pumpkin pie spice paired with maple syrup creates the best sweet pumpkin flavor.

Vanilla bean powder is my go-to when baking muffins. It is a pure form of vanilla made from vanilla beans. If you don’t have vanilla powder you can use vanilla extract. In place of 1 tsp vanilla powder, you will need 2 tsp of pure vanilla extract.

This recipe calls for dark chocolate chips. Many chocolate chips have added sugar, or milk. My favorite chips to use are these dark cacao chips. They are dairy free and made from real cacao. Keep in mind that dark cacao chips are not as sweet at traditional chocolate chips. My kids think this is fake chocolate, when in reality is more real than anything.

ingredients to make Pumpkin Chocolate Chip Muffins

You will also need a muffin tin, muffin liners, and a hand mixer to make this healthy pumpkin chocolate chip muffin recipe. Check out my healthy cooking essentials for everything you need when baking muffins.

I mention it all the time, so you know by now that I have a huge sweet tooth I always tend to have snacks on hand. But I am also a pretty strict eater as far as eating healthy. At any given time I have a stash of healthy muffins, or snacks in my house. Some in the fridge, others in the freezer for later.

How to Make Healthy Chocolate Chip Pumpkin Muffins

First, preheat the oven to 350 degrees F.

Then combine the coconut flour with the pumpkin pie spice, salt, and baking soda and set aside.

In a separate large bowl, add the pumpkin puree and the eggs. Make sure to use pure pumpkin puree where the only ingredient is pumpkin.

pure pumpkin puree and raw eggs

Next, add the maple syrup and the melted coconut oil to the bowl.

add coconut oil to wet ingredients

Use a stand mixer, or hand mixer and mix the wet ingredients until smooth.

hand mix batter of wet ingredients

Then add the dry ingredients into the bowl with the wet ingredients.

coconut flour gluten free pumpkin muffins

Blend again until thoroughly combined and smooth.

kitchen aid hand mixer to mix until smooth

Then fold in the chocolate chips to the muffin batter.

dark chocolate cacao chips

How to Bake Healthy Pumpkin Chocolate Muffins

First, line a muffin pan with paper liners.

parchment paper liners and muffin batter

Then scoop even amounts of muffin batter into each of the muffin cups.

Sprinkle a few of the remaining dark chocolate chips on top of each muffin.

pumpkin muffins with chocolate chips

Bake for 22-24 minutes or until they pass the toothpick test. Poke a clean toothpick into the center of a muffin, and if it comes out clean then the muffins are done. I start checking the muffins with a toothpick around 18 minutes and go from there.

oven baked healthy muffin recipe

Remove the healthy pumpkin chocolate chip muffins and place on a wire rack to cool.

Let them cool for at least 5 minutes before you remove them from pan to cool on the cooling rack. Often, as they cool the parchment paper liners will start to separate from the muffins.

muffins cooling on a wire rack

Delicious Homemade Pumpkin Muffins

Enjoy these tasty muffins as an afternoon snack, or an after school snack for the kids.

close up of melted chocolate in pumpkin muffin

These muffins are light and moist, like cake. They are naturally sweetened and a perfect balance of pumpkin and chocolate.

top view of pumpkin chocolate muffins on platter

These muffins pair nicely with a cup of coffee or tea, in the morning or later in the day.

chocolate chip pumpkin muffin with morning coffee

Healthier pumpkin chocolate chip muffins are a great option when you want something quick and easy and not filled with crappy ingredients.

best Pumpkin Chocolate Chip Muffins healthy

The light cake like texture makes this the perfect treat to satisfy your sweet tooth without filling you up.

Pumpkin Chocolate Chip Muffins moist like cake

Store leftover muffins in an airtight container in the refrigerator for 3-5 days. They also freeze well for later.

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For more healthy muffin recipes check out:

Pumpkin Chocolate Chip Muffins Recipe

Pumpkin Chocolate Chip Muffins Recipe

Yield: 10
Prep Time: 10 minutes
Cook Time: 22 minutes
Total Time: 32 minutes

Fill the kitchen with the aroma of pumpkin with these healthy pumpkin chocolate chip muffins.


  • 1/4 cup coconut flour
  • 1 tsp baking soda
  • 4 tsp pumpkin pie spice
  • 1/4 tsp salt
  • 4 large eggs
  • 1/4 cup coconut oil, melted
  • 1 cup pumpkin puree
  • 1/2 pure maple syrup
  • 1/2 dark chocolate chips + 2 Tbsp for tops of muffins
  • 1 tsp pure vanilla bean powder


  1. First, preheat the oven to 350F
  2. In a medium bowl, sift together the coconut flour, baking soda, pumpkin pie spice, vanilla powder, and salt and keep aside.
  3. In a separate large bowl. add the eggs, coconut oil, maple syrup, and pumpkin puree, and mix with a hand mixer until smooth.
  4. Add the dry ingredients into the bowl and blend until the batter is well combined.
  5. Fold in the chocolate chips.
  6. Line a muffin pan with paper liners.
  7. Scoop even amounts of muffin batter into each of the muffin cups.
  8. Top with remaining chocoalte chips.
  9. Bake for about 22-24 minutes, or until golden. Test with a toothpick. Let the muffins cool in the pan for 5 minutes. Transfer to a wire rack to cool completely.
Nutrition Information:
Yield: 10 Serving Size: 6 Servings
Amount Per Serving: Calories: 125Total Fat: 9gSaturated Fat: 6gTrans Fat: 0gUnsaturated Fat: 2gCholesterol: 76mgSodium: 230mgCarbohydrates: 8gFiber: 2gSugar: 4gProtein: 4g

nutritional values may vary

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Pumpkin Chocolate Chip Muffins recipe

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