Healthy pumpkin chocolate chip muffins are sure to be a fall favorite! They’re made with whole wheat flour and flecked with dark chocolate chips for a wholesome spin, perfect as a light breakfast or snack.

Recipe Overview

Why you’ll love it:  These healthy pumpkin chocolate chip muffins are so fluffy and full of fall flavor. Besides, isn’t anything with chocolate chips something to love? I think so!

How long it takes: 15 minutes to prep, 23 minutes to bake
Equipment you’ll need: a mixing bowl, measuring utensils. muffin tin, oven
Servings: 12 muffins

Two pumpkin chocolate chip muffins stacked on a small white plate, with more muffins in the background.
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Healthy Pumpkin Chocolate Chip Muffins

Ben and the kids LOVE these pumpkin chocolate chip muffins. My kids deemed me the best at making muffins, better than Grandma! Grandma is THE muffin maker and always has homemade muffins for the kids. Sorry, mom. I think they were influenced by the oversized chocolate chips this time. I’ll let you keep the crown.

These pumpkin chocolate chip muffins are pretty hard to resist. They’re moist, fluffy, made with whole wheat flour, real pumpkin purée, and loaded with dark chocolate. It’s a healthier spin that’s still filled with flavor, perfect for guilt-free snacking!

Why You’ll Love This Pumpkin Muffin Recipe

  • Healthier. This pumpkin chocolate chip muffin recipe got a health-conscious makeover. Goodbye, refined sugar. Hello, pure maple syrup (and lots of fall flavor!). And of course, there’s whole wheat flour to add nutrition and fiber.
  • Dark chocolate chips. The chocolate chips add just the right amount of sweetness, and they are everywhere in and outside of these healthy pumpkin chocolate chip muffins!
  • Low in fat. There’s very little added fat because these pumpkin chocolate chip muffins get plenty of moisture from the pumpkin purée, along with unsweetened applesauce.
Close up overhead view of muffins in a tin.

Is Canned Pumpkin Good For You?

Canned pumpkin is highly nutritious and rich in vitamins (especially vitamin A) and loaded with healthy minerals (Healthline). To top it off, pumpkin is low in calories! Pumpkin is usually associated with fall, but I’ll use pumpkin in recipes like healthy pumpkin bread and pumpkin chocolate chip bread, and these wholesome whole-wheat pumpkin chocolate chip muffins year-round.

Overhead view of ingredients for pumpkin chocolate chip muffins.

What You’ll Need

I’ll get you started with a few notes on the key ingredients for these healthy chocolate chip pumpkin muffins. Scroll to the printable recipe card with complete instructions, measurements, and nutrition information.

  • Canned Pumpkin Puree: Make sure to use pure 100% canned pumpkin. Don’t mistakenly buy canned pumpkin pie filling, as it has added sugar and spices. The two ingredients aren’t interchangeable.
  • Eggs: A couple of large eggs add protein and help bind the muffins together.
  • Unsweetened Applesauce: I often use applesauce in my muffins to replace some of the oil or butter. You won’t be able to tell the difference! One snack-size applesauce is just the right amount.
  • Pure Maple Syrup: Use the real thing! 100% pure maple syrup, or bust. This is not the recipe for artificial pancake syrup.
  • Coconut Oil: Coconut oil solidifies so you’ll have to melt it first. Good substitutes are melted butter, or any type of mild-tasting oil. You’ll only need a quarter cup.
  • Pure Vanilla Extract: Added for sweet-tasting flavor.
  • Whole Wheat Flour and All-Purpose Flour: Use a mixture of both types of flour if you can. All whole wheat flour can make the muffins rather heavy and dense. They will turn out fine if you use only all-purpose but why not add a little extra nutrition?
  • Baking Powder, Baking Soda, Salt: Normal muffin stuff for leavening and flavor.
  • Pumpkin Pie Spice: I always make my own pumpkin pie spice blend but you can buy it pre-made as well. If you’d rather, just substitute plain ground cinnamon.

How To Make Pumpkin Chocolate Chip Muffins

Another thing to love? This is an easy one-bowl recipe! Find a nice big bowl, get the oven preheating to 400ºF, and grease a muffin tin. This recipe makes 12 muffins.

  • Combine the wet ingredients. Start by mixing together the wet ingredients: eggs (give them a little stir first to break up the yolks), pumpkin, applesauce, maple syrup, coconut oil, and vanilla. Whisk until the mixture is nice and smooth.
  • Next, add the dry ingredients. Start with the two kinds of flour, then add the baking powder, baking soda, salt, and pumpkin pie spice. When all the dry ingredients are in the bowl sitting on top of the wet ingredients, lightly stir the dry ingredients until they are just mixed together on the surface, and then stir the dry mixture into the batter.
  • Add the chocolate chips. Once the batter is combined, fold in the chocolate chips.

Make It a One-Bowl Recipe

Lightly whisking the dry ingredients together while they’re sitting on top of the wet batter is an easy way to make this recipe all in one bowl. I love this little trick. Many recipes use another bowl to mix the dry ingredients before adding them to the wet ingredients, but why make another bowl dirty? This “hack” works just fine!
  • Fill the pan. Scoop the batter equally into the muffin cups and sprinkle a few extra chips on top of the batter if you want. Those chips are just a promise of all the goodness inside.
  • Bake. Bake the muffins until a toothpick inserted in the center comes out clean or with a crumb or two attached. If the toothpick comes out sticky with batter, bake the muffins for a couple more minutes and test again.
One pumpkin chocolate chip muffin on a small white plate, more muffins in the background.

Tips for Success

Keep these tips in mind for the best homemade pumpkin chocolate chip muffins:

  • Make sure there aren’t any dry pockets of flour but don’t beat the batter like crazy either. Just stir it until it’s blended, nothing more. Overmixing leads to tough, flat muffins with large holes in them. Yikes, you don’t want that!
  • Wait until the muffins are completely cool before storing them. Storing muffins airtight while they’re still warm leads to condensation, which will cause the muffins to become sticky and soggy.


Is canned pumpkin the same as pumpkin puree?

Canned pumpkin and pumpkin purée are the same thing. Both are 100% pumpkin, with nothing added to it. Canned pumpkin is not the same as pumpkin pie filling, however, which should only be used for pumpkin pie.

What’s in pumpkin pie spice?

Most pumpkin pie spice blends contain cinnamon, nutmeg, ginger, allspice, and cloves. It’s also sometimes called “mixed spice” in the grocery store spice aisle.

How many carbs are in a pumpkin chocolate chip muffin?

These lightened-up pumpkin chocolate chip muffins have 28g of carbs. Find complete nutritional information in the recipe card below.

Overhead view of pumpkin chocolate chip muffins in a muffin pan, with two muffins missing.

Make This Muffin Recipe Your Own

There are so many ways that you can customize your healthy pumpkin chocolate chip muffins depending on your family’s tastes. Here are some easy variation ideas:

  • Substitute milk chocolate chips, mini chocolate chips, white chocolate chips, or whatever your favorite is for the semi-sweet chips.
  • Substitute chopped nuts for the chocolate chips, or include both! Chopped pecans or walnuts are good choices. Dried fruit is good, too, like raisins, cranberries, or cherries.
  • Not crazy about whole wheat? Simply use all-purpose flour instead of whole wheat flour.
  • Looking for even more fiber? You’ll love pumpkin bran muffins with whole wheat flour and bran flakes.
  • Like a more savory muffin? Try pumpkin cheddar muffins.
  • Use a gluten-free flour, like Bob’s Red Mill Gluten Free 1-to-1 Baking Flour, if you prefer. Note: I haven’t tested this recipe with gluten-free flour.
  • Love pumpkin? Try pumpkin dip (it’s great with graham crackers and apple slices) or pumpkin poke cake for an easy fall dessert.

Ways to Serve Pumpkin Chocolate Chip Muffins

Enjoy your fluffy pumpkin chocolate chip muffins with a smear of butter or a drizzle of honey or maple syrup. I’m pretty sure you’re going to want to eat one right away, nice and toasty out of the oven. Why not make a cup of coffee or homemade hot chocolate to go with it? This ginger-spiced hot chocolate is perfect with a pumpkin muffin!

These easy muffins make a great addition to a fall brunch spread, alongside nutritious baked oatmeal and a cozy breakfast casserole. Of course, we can’t forget the mimosas.

How to Store

  • To Store: Store pumpkin chocolate chip muffins at room temperature for up to 4 days. Store them in an airtight container or resealable bag. If you want them to last even longer; store them in the refrigerator for up to 1 week.
  • Freezer: These muffins freeze beautifully, too. Use a freezer-safe container or bag. I like to freeze them in individual bags because they make a great lunchbox treat. They thaw quickly at room temperature.

Why not bake a double batch? It’s just as easy to make twice as many healthy muffins and then you’ll have extra to freeze!

More Easy Muffin Recipes


Pumpkin Chocolate Chip Muffins

4.84 from 6 votes
Prep: 15 minutes
Cook: 23 minutes
Total: 38 minutes
Servings: 12 muffins
Healthy pumpkin chocolate chip muffins are a favorite fall treat! These fluffy and wholesome pumpkin muffins loaded with chocolate chips are an easy snack or quick breakfast.
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  • 1 can (15 oz.) pumpkin puree (not pumpkin pie filling)
  • 2 large eggs, beaten
  • ½ cup unsweetened applesauce
  • ¼ cup maple syrup
  • ¼ cup melted coconut oil (see note)
  • 1 teaspoon pure vanilla extract
  • 1 cup whole wheat flour
  • ¾ cup all-purpose flour
  • 1 teaspoon baking soda
  • 1 teaspoon baking powder
  • 1 teaspoon pumpkin pie spice
  • ½ teaspoon salt
  • ¾ cup dark chocolate (semi-sweet) chips, more for topping if desired


  • Preheat oven to 400°F. Spray a 12 cup muffin tin with nonstick cooking spray or line with paper liners.
  • In a large bowl, whisk together pumpkin puree, eggs, applesauce, maple syrup, coconut oil, and vanilla extract.
  • 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.
  • Fold in chocolate chips.
  • Scoop batter into prepared muffin pan. Top with additional chocolate chips, if desired.
  • Bake for 19 to 23 minutes or until a toothpick inserted in the middle of one of the muffins comes out clean or with crumbs.
  • Let cool 4 to 5 minutes in pan before removing from pan onto a rack to cool completely.


  • If desired, replace the coconut oil with melted butter or another mild tasting oil.
  • Chopped nuts, milk chocolate chips, white chocolate chips, or mini chocolate chips can be substituted for the semi-sweet chips. Raisins, dried cranberries or cherries are good, too.
  • For more pumpkin pie flavor, increase the amount of the pumpkin pie spice to 1 ½ teaspoons. Or, if you’re out of pumpkin pie spice, just substitute a teaspoon of cinnamon instead.
  • 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.



Serving: 1muffin, Calories: 209kcal, Carbohydrates: 28g, Protein: 4g, Fat: 9g, Saturated Fat: 8g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 1g, Trans Fat: 1g, Cholesterol: 27mg, Sodium: 249mg, Potassium: 223mg, Fiber: 3g, Sugar: 10g, Vitamin A: 5557IU, Vitamin C: 2mg, Calcium: 81mg, Iron: 2mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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4.84 from 6 votes (6 ratings without comment)

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  1. denise says:

    sounds easy and tasty

    1. Rachel Gurk says:

      For sure!

  2. Onkar Bhosale says:

    Thank you for a beautiful chocolate chip muffins recipe. Made this tonight for my family and the kitchen smells divine. It tastes even better.

    1. Rachel Gurk says:

      I’m so happy to hear that you love this recipe! Thanks for taking the time to come back and leave a comment!