Extra soft and moist Pumpkin Chocolate Chip Muffins made with a full can of pumpkin puree and dotted with chocolate chips. Rise and shine with a healthy breakfast!

In the fall, we also make mornings easy with these healthy pumpkin muffins, healthy chocolate chip muffins and banana pumpkin muffins.

12 pumpkin chocolate chip muffins and a few chocolate chips around them with linen towel on a countertop.

Any healthy muffin sweetened with chocolate chips is a winner in this household, and these pumpkin chocolate chip muffins are the best! Rich pumpkin, warm fall spices, and gooey chocolate belong together.

This recipe came from my popular healthy pumpkin chocolate chip bread, I added a splash of vanilla and made irresistible bakery-style muffins.

Why You’ll Love This Recipe

  • No leftover pumpkin puree: Just like with healthy pumpkin bread, we rely on an entire can to make these muffins moist.
  • Your choice of flour: Different types of flour that work with this recipe include whole wheat flour, spelt flour, whole wheat pastry flour or white whole wheat flour.
  • Refined sugar free: Chocolate chip pumpkin muffins are fluffy and delicious with no added sugar, except chocolate chips. They taste decadent and make the perfect healthy snack or healthy dessert.
  • Easy: All the prep is done in one bowl! No mixer needed, easy to make, and easy clean up.
  • Moist: No dry muffins here! A full can of pumpkin puree adds sweetness and moisture. And if you love everything pumpkin, homemade pumpkin puree is perfect for all your fall goodies.

Ingredients for Pumpkin Chocolate Chip Muffins

This pumpkin chocolate chip muffins recipe is made with simple, pantry friendly ingredients. You can enjoy them now and throughout the year.

Pumpkin puree, whole wheat flour, maple syrup, eggs, chocolate chips, pumpkin pie spice, baking powder, baking soda, vanilla, oil and salt.
  • Eggs: Add structure to the muffins.
  • Pumpkin puree: You’ll need the standard 15 ounces canned pumpkin, make sure to get pumpkin puree and not pumpkin pie filling. You can also use homemade pumpkin puree, it’s so easy! Here’s how to cook a pumpkin and make puree out of it, I like to keep it in the fridge for all my fall baking.
  • Liquid sweetener: These healthy pumpkin chocolate chip muffins are naturally sweetened with maple syrup or honey. Other liquid sweeteners would work too, but taste will be different.
  • Oil: Stick to a mild oil like avocado oil or olive oil. You could substitute with the same amount of melted coconut oil or melted unsalted butter.
  • Pumpkin pie spice: This warm spice helps deepen the pumpkin flavor. I like to make my own pumpkin pie spice substitute but you can use store-bought too.
  • Vanilla: Pure vanilla extract adds a deep, warm flavor and transforms these muffins from delicious to irresistible.
  • Baking essentials: As always you’ll need baking powder, baking soda, and salt to help muffins rise, have structure, and enhance the other flavors.
  • Flour: I’m all about using wholesome ingredients in my healthy muffins recipes, I recommend whole wheat flour or spelt flour. But you can also use white flour.
  • Chocolate chips: I used dark chocolate chips but feel free to add semisweet chocolate chips, milk chocolate chips, or mini chocolate chips instead.

How to Make Pumpkin Chocolate Chip Muffins

Bite into freshly baked pumpkin chocolate chip muffins in under an hour! Grab a bowl, mix your wet ingredients with dry ingredients and bake, it’s that easy.

Here’s a quick photo overview, there’s also a full recipe card below.

Step  process how to make pumpkin chocolate chip muffins from scratch.

Start by preheating your oven to 425 F and spraying a 12 cup muffin tin.

  • Make the batter: To a large bowl, add eggs, pumpkin puree, maple syrup, oil, pumpkin pie spice, vanilla extract, baking powder, baking soda and salt. Whisk to combine until no white lumps are visible. Next, add the flour and gently mix just enough until combined.
  • Add chocolate chips: Fold in the chocolate chips until evenly incorporated so each bite is loaded with chocolate-y goodness.
  • Fill the prepared muffin pan: Evenly distribute the batter, I always use my trigger ice cream scoop.
  • Bake: Set them in the preheated oven and bake for 7 minutes, we start baking at a higher temperature for bakery-style dome top muffins. Then reduce to 375 F and bake for another 10-11 minutes or until a toothpick comes out mostly clean, a few moist crumbs is OK.

Tips for Best Results

These tips help make this pumpkin chocolate chip muffin recipe the best.

  • To substitute pumpkin pie spice: If you find yourself without pumpkin pie spice, add 1 teaspoon of cinnamon and 1/4 teaspoon each of ginger, nutmeg, cloves, and allspice. Or up to 3 teaspoons of just cinnamon.
  • Flours that will work: Choose from whole wheat flour, spelt flour, white whole wheat flour, or all-purpose flour.
  • Don’t use dry sweetener: I’ve created this recipe with the perfect wet to dry ratio therefore, granulated sugar will not work.
  • Add more chocolate chips on top: I decided to add 3 extra chocolate chips on top each muffin to make them prettier.
  • Measure flour correctly: If too much flour is added, your muffins will be dry. Scoop and level is the best way to correctly measure flour – scoop the flour into the measuring cup then level off with the flat edge of a knife.
  • Don’t over bake the muffins: Remember all ovens and pans vary, it’s important to remove your muffins as soon as a toothpick inserted in the middle comes out clean.
  • Use liners or skip: These muffins don’t stick and are easy to remove. Feel free to use parchment paper liners or skip all together.
Chocolate chip pumpkin muffins in a muffin tin. Linen towel and chocolate chips on a counter.


  • Add streusel: Make a crumb topping by mixing flour, sugar and butter together, just as I did for these raspberry muffins.
  • Cinnamon sugar topping: Cinnamon and pumpkin are the perfect pair, and I loved the sweet topping on apple cinnamon muffins, so why not try it here?! Just whisk brown sugar and cinnamon together in a small bowl, brush the top of the muffin with melted butter or coconut oil, and dip the muffin until coated.
  • Cream cheese: Add a creamy filling by swirling 1-2 teaspoons of cream cheese in the middle, follow the same method in healthy pumpkin muffins. This is sure to satisfy your craving for a Starbucks pumpkin cream cheese muffin.
  • Add texture: Go crazy with add-ins and mix whatever you like into the pumpkin mixture. Try pecans, walnuts, dried cranberries, raisins, or toasted coconut. You could also sprinkle pumpkin seeds or oats on top before baking.
  • Spread: For breakfast and afternoon snacking I love spreading peanut butter or nut butter on top for extra protein.
  • Switch up the chocolate chips: Try white chocolate chips or butterscotch chips instead.

How to Store

Store: Once cooled, place muffins in a resealable bag or airtight container and store them at room temperature for 3 days, this will keep them moist. If you notice they get too moist, keep the lid ajar a bit.

Freeze: Transfer to an airtight container and pop them in the freezer for up to 3 months.

Storage Tip

For more storage tips and tricks, check out my detailed post how to store muffins and how to freeze muffins.


Can I make these muffins with gluten-free flour?

Not for this recipe. You could try to substitute 1:1 ratio of all-purpose gluten free flour, however in my experience it needs a bit more liquids, give it a try and let me know!

Can I prepare the batter ahead of time?

Yes. Make the batter, leaving out the leveling agents, cover tightly and refrigerate for up to 24 hours. Add in baking powder and baking soda and bake as per recipe.

What can I use instead of pumpkin puree?

Pureed butternut squash, acorn squash, or sweet potatoes are great substitutes for pumpkin puree.

Can I make mini pumpkin chocolate chip muffins?

To make mini pumpkin chocolate chip muffins, you’ll need to decrease the baking time to 10-12 minutes, and do a toothpick test.

Can I turn this recipe into a loaf?

Yes! Preheat your oven to 350 degrees F and bake for 50-60 minutes. You could also make mini loaves and bake for 25-30 minutes.

More Pumpkin Recipes to Try

Person holding bitten pumpkin chocolate chip muffin showing texture and melted chocolate inside.
12 pumpkin chocolate chip muffins and a few chocolate chips around them with linen towel on a countertop.

Pumpkin Chocolate Chip Muffins

Extra soft and moist Pumpkin Chocolate Chip Muffins made with a full can of pumpkin puree and dotted with chocolate chips.
4.34 from 6 votes
Servings 12 muffins
Calories 256
Diet Low Fat
Prep Time 10 minutes
Cook Time 17 minutes
Resting Time 10 minutes
Total Time 37 minutes



  • Preheat oven to 425 degrees F and spray muffin tin with cooking spray. Set aside.
  • In a large mixing bowl, add eggs, pumpkin puree, maple syrup, oil, pumpkin pie spice, vanilla extract, baking powder, baking soda and salt; whisk well to combine. Add flour and gently mix until combined. Then fold in the chocolate chips.
  • Using an ice cream scoop, distribute batter evenly between 12 openings of a muffin tin. I added 3 more chocolate chips on top of each muffin.
  • Bake at 425 F for 7 minutes, then reduce heat to 375 and bake for another 10-11 minutes or until a toothpick inserted in the center comes out clean.
  • Remove muffins from the oven, let them cool for 5 minutes and transfer to a cooling rack to cool off for another 10 minutes. Enjoy!


  • Store: To prevent muffins from drying, place in a resealable bag or airtight container and store on a counter for 3 days. If you notice they get too moist, keep the lid of a container ajar a bit.
  • Freeze: In an airtight container for up to 3 months.
  • Substitute pumpkin spice blend: Use 1 teaspoon cinnamon and 1/4 teaspoon each of ginger, nutmeg, cloves and allspice. Alternately, use 2-3 teaspoon of cinnamon if you are out of all other spices.
  • Other flours: You can use the same ratio of whole wheat pastry flour or white whole wheat flour.


Serving: 1muffin | Calories: 256kcal | Carbohydrates: 38g | Protein: 6g | Fat: 10g | Saturated Fat: 5g | Trans Fat: 0.003g | Cholesterol: 31mg | Sodium: 291mg | Fiber: 4g | Sugar: 15g
Course: Muffins
Cuisine: North American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

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About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

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    1. Not sure which ingredient or part you found to taste like “cardboard”…all simple ingredients I use in all muffin recipes that we love and readers enjoy too. Also I never ate cardboard, so could never imagine calling any food tasting like it. I guess to each their own and you could try other’s recipes.

  1. 4 stars
    Hi Olena!
    These look good and I plan to make them soon. I have a question: Is 2 TABLESPOONS pumpkin spice correct? or is it 2 teaspoons?
    Your muffins are delicious, thanks!

  2. 5 stars
    Thank you! Baked two batches of these with homemade pumpkin puree and homebade pumpkin spice! So soft and finally a recipe without enormous amount of sweeteners!

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