Flavorful pumpkin chocolate chip muffins flecked with dark chocolate chips are going to become a fall favorite! Use whole wheat flour to make them healthier and give them a great nutty flavor! 

Pumpkin chocolate chip muffins in a basket with orange towel.

As promised…time for a fall recipe. I think it’s time for a good pumpkin muffin recipe. I’ve shared healthy pumpkin bread, pumpkin streusel bread, and pumpkin chocolate chip bread, but we haven’t done muffins yet! 

Side note: I know that pumpkin is usually associated with fall (think Halloween treats and Thanksgiving pumpkin pies). Well, I actually think that pumpkin is delicious year round. Canned pumpkin is available in grocery stores whatever the season and it’s so nutritious, rich in vitamins and minerals and low in calories. I love this good-for-you pumpkin curry soup for a healthy lunch (it only takes 20 minutes to make!).

So why wait for fall to make these delicious pumpkin chocolate chip muffins?

A muffin pan full of pumpkin muffins flecked with chocolate chips. Orange fabric is pictured in the background.

My kids and Ben love these muffins. My kids deemed me the best at making muffins, better than grandma! Grandma is THE muffin maker and always has muffins for the kids. Sorry, mom. I think they were influenced by the over-sized chocolate chips, if we’re being honest. I’ll let you keep the crown.

Overhead view of a 12-cup muffin tin filled with orange colored muffins sprinkled with chocolate chips.

Ben doesn’t love pumpkin-flavored things, and said these didn’t really taste like pumpkin. With that being said, if you want a little more pumpkin flavor, bump up the amount of pumpkin spice you use in this recipe and it will really make those fall flavors pop.

About these pumpkin chocolate chip muffins

I like to make these muffins a little better for you by using a mix of whole wheat flour and all-purpose flour. I also sweeten them naturally with a combination of maple syrup and applesauce. You’ll also find coconut oil in these muffins. You could substitute other oils or make these with butter, but I do love the coconut oil in these muffins.

Close up view of muffins in a basket. They are orange in color and sprinkled with chocolate chips.

You’re going to love these so much that you’ll probably want to make a double batch! You won’t be sorry.

Tip: Don’t forget, you can always substitute store bought spice for my homemade pumpkin pie spice.

A muffin tin filled with chocolate chip pumpkin muffins.

Pumpkin chocolate chip muffins in a basket with orange towel.

Pumpkin Chocolate Chip Muffins

Yield: 12 muffins
Prep Time: 15 minutes
Cook Time: 23 minutes
Total Time: 38 minutes

Flavorful pumpkin chocolate chip muffins flecked with dark chocolate chips are going to become a fall favorite! Use whole wheat flour to make them healthier and give them a great nutty flavor! 


  • 1 (15 oz) can pumpkin puree
  • 2 large eggs, beaten
  • 1/2 cup unsweetened applesauce
  • 1/4 cup maple syrup
  • 1/4 cup melted coconut oil
  • 1 teaspoon pure vanilla extract
  • 1 cup whole wheat flour
  • 3/4 cup all-purpose flour
  • 1 teaspoon baking soda
  • 1 teaspoon baking powder
  • 1 teaspoon pumpkin pie spice
  • 1/2 teaspoon salt
  • 3/4 cup dark chocolate chips, more for topping if desired


  1. Preheat oven to 400°F. Spray a 12 cup muffin tin with nonstick cooking spray or line with paper liners.
  2. In a large bowl, whisk together pumpkin puree, eggs, applesauce, maple syrup, coconut oil, and vanilla extract.
  3. On top of wet ingredients, add dry ingredients: Whole wheat flour, all-purpose flour, baking soda, baking powder, pumpkin pie spice, salt. Mix together dry ingredients gently before mixing dry ingredients into wet ingredients. Stir until combined, do not overmix.
  4. Fold in chocolate chips.
  5. Scoop batter into prepared muffin pan. Top with additional chocolate chips, if desired.
  6. Bake for 19-23 minutes or until a toothpick inserted in the middle of one of the muffins comes out clean or with crumbs.
  7. Let cool 4-5 minutes in pan before removing from pan onto a rack to cool completely.


  • You could replace the coconut oil with butter or another mild tasting oil.
  • If desired, you could substitute nuts, milk chocolate chips, or mini chocolate chips for the semi-sweet chips.
  • Increase the amount of the pumpkin pie spice to 1 1/2 teaspoons for more pumpkin pie flavor.
  • This recipe is written for plain canned pumpkin. Don't use canned pumpkin pie filling because it contains sugar, spices, etc. already and the recipe won't turn out.
Nutrition Information:
Yield: 12 Serving Size: 1 muffin
Amount Per Serving: Calories: 203Total Fat: 9gSaturated Fat: 6gTrans Fat: 0gUnsaturated Fat: 2gCholesterol: 32mgSodium: 250mgCarbohydrates: 27gFiber: 3gSugar: 11gProtein: 4g

RachelCooks.com sometimes provides nutritional information, but these figures should be considered estimates, as they are not calculated by a registered dietitian. Please consult a medical professional for any specific nutrition, diet, or allergy advice.

Did you make this recipe?

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Verdict: I’m a sucker for anything with dark chocolate, and these muffins are no exception.
Husband’s take: Ben loved these muffins, and so did the kids.
Changes I would make: None at all! But if you prefer a different kind of chocolate, you could try these with semisweet or milk chocolate. Or you could use nuts instead of chocolate. Or you could leave them out altogether. Do your thing!
Difficulty: Easy!