If you love pumpkin chocolate chip muffins but want a healthy version, this easy recipe is for you! These muffins are made with simple, wholesome ingredients that keep them both tasty and good for you. Whether you’re looking for a snack or a quick breakfast, these muffins are easy to make and full of fall flavor.

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Ingredients Needed to Bake Pumpkin Chocolate Chip Muffins
- 1 cup pumpkin puree
- 2 large eggs
- 1/4 cup pure maple syrup or honey
- 1/4 cup coconut oil, melted (I use Kirkland)
- 1/4 cup unsweetened milk of your choice
- 1 tsp vanilla extract
- 2 tsp ground cinnamon
- 1/4 tsp ground nutmeg
- 1/4 tsp ground ginger
- 1/8 tsp ground cloves
- 1/2 tsp baking soda
- 1 tsp baking powder
- 1/4 tsp salt
- 1/4 cup chopped walnuts or pecans (optional)
- 1/4 cup dark chocolate chips
- 1 1/2 cups whole wheat flour

Ingredients Needed to Make Oats and Cinnamon Sugar Crumble Topping
- 1/4 cup rolled oats
- 2 tbsp brown sugar (substitute for coconut sugar)
- 1/2 tsp ground cinnamon
- 1 tbsp melted butter or coconut oil
- Pinch of salt (optional)
Variations to This Pumpkin Chocolate Chip Muffin Recipe
Gluten-Free Option:
Use 1 1/2 cups gluten-free flour blend (be sure it’s a blend with xanthan gum).
Dairy-Free Version:
Use dairy-free chocolate chips and plant-based milk to make the recipe completely dairy-free.
Oat Flour Option:
Swap out the whole wheat flour with 1 1/2 cups of oat flour for a slightly different texture and added fiber.
Lower-Sugar Option:
Reduce the amount of maple syrup or honey to 2-3 tablespoons and increase the spices slightly for extra flavor without the added sweetness.
These variations let you customize the pumpkin chocolate chip muffins to your dietary preferences while keeping them delicious and healthy!

Tips for Making The Best Pumpkin Chocolate Chip Muffins
- Don’t Overmix: Stir the batter just until combined to keep the muffins light and fluffy.
- Use Room Temperature Ingredients: This helps everything mix together more smoothly.
- Customize Add-ins: Adjust the amount of chocolate chips or nuts based on your preference.
- Check Doneness: Insert a toothpick or cake tester in the center – if it comes out clean, they’re done!
- Let Them Cool: Allow muffins to cool in the pan for a few minutes before transferring to a wire rack.
These tips will help you get the best results from your pumpkin chocolate chip muffins!
Equipment Needed for This Recipe
- Mixing Bowls
- Whisk or Spoon
- Muffin Tin – Standard 12-cup muffin tin.
- Muffin Liners or Non-Stick Spray
- Measuring Cups and Spoons
- Spatula
- Toothpick or Cake Tester

How to Make These Healthy Pumpkin Chocolate Chip Muffins
- Preheat the Oven: Set your oven to 350°F (175°C) and line a 12-cup muffin tin with liners or spray with non-stick spray.
- Mix Wet Ingredients: In a large bowl, whisk together the pumpkin puree, eggs, maple syrup (or honey), melted coconut oil, milk, and vanilla extract until smooth.
- Combine Dry Ingredients: In a separate bowl, mix the whole wheat flour, cinnamon, nutmeg, ginger, cloves, baking soda, baking powder, and salt.
- Combine Wet and Dry Ingredients: Gradually add the dry ingredients to the wet ingredients, stirring gently until just combined. Be careful not to overmix!
- Add Extras: Fold in the dark chocolate chips and chopped walnuts or pecans if using.
- Fill Muffin Tin: Evenly divide the batter between the muffin cups, filling each about 3/4 full.
- Bake: Place the muffin tin in the oven and bake for 18-22 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
- Cool and Enjoy: Let the muffins cool in the pan for a few minutes before transferring them to a wire rack to cool completely.
How to Make The Oats and Cinnamon Sugar Crumble Topping
- In a small bowl, combine the oats, brown sugar, cinnamon, and a pinch of salt (if using).
- Pour in the melted butter or coconut oil and mix until the ingredients are fully coated and crumbly.
- Sprinkle the mixture evenly over the muffin batter before baking.
- Bake the muffins as directed, and the crumble will create a sweet, crunchy topping.
This topping adds a delightful, slightly crispy texture and a warm cinnamon-sugar flavor to pumpkin chocolate chip muffins! It is so good!

How to Store Your Pumpkin Chocolate Chip Muffins
To keep your pumpkin chocolate chip muffins fresh, here’s how I recommend storing them:
- At Room Temperature: Store the muffins in an airtight container for up to 3 days. Make sure they are fully cooled before storing to avoid moisture buildup.
- In the Refrigerator: If you want them to last a bit longer, place the pumpkin chocolate chip muffins in an airtight container and refrigerate for up to a week. You can warm them slightly before eating.
- Freezing: For longer storage, wrap the muffins individually in plastic wrap and place them in a freezer-safe bag. They can be frozen for up to 3 months. Thaw them at room temperature or pop them in the microwave for a quick warm-up.
These methods help maintain their moisture and flavor!
FAQ’s
How long do pumpkin muffins last?
Pumpkin muffins last about 3 days at room temperature in an airtight container, up to a week in the fridge, and up to 3 months in the freezer.

How do you reheat pumpkin muffins?
You can reheat pumpkin muffins in the microwave for 15-20 seconds or in the oven at 300°F (150°C) for about 5-10 minutes until warmed through.
Can you freeze pumpkin chocolate chip muffins?
Yes, you can freeze pumpkin muffins! Wrap them individually in plastic wrap and store them in a freezer-safe bag for up to 3 months. Thaw them at room temperature or reheat them straight from frozen.
More Delicious Recipes
Personalize Your Fall Baking with Printable Recipe Cards and Tags!
Want to bake these pumpkin chocolate chip muffins and share them with friends or family? Why not make your baked gifts extra-special with my printable fall recipe cards and baked goods gift tags? These beautifully designed cards are perfect for writing down your favorite recipes, and the gift tags add a charming touch to any homemade treat. They’re available in fall-inspired colors like rust, green, and gray-brown—ideal for the season!
Grab them in my Etsy shop and make your baked gifts even more thoughtful!

Pumpkin Chocolate Chip Muffins – A Healthy Recipe
Equipment
- Mixing bowls
- Whisk or Spoon
- muffin tin (standard 12 muffin tin)
- Muffin Liners or Non-Stick Spray
- Measuring Cups and Measuring Spoons
- Spatula
- Toothpick or Cake Tester
Ingredients
- 1 cup Pumpkin puree
- 2 Large eggs
- ¼ cup Pure maple syrup or honey
- ¼ cup Coconut oil, melted
- ¼ cup Milk (any kind of milk is fine)
- 1 tsp Vanilla extract
- 2 tsp Ground cinnamon
- ¼ tsp Ground nutmeg
- ¼ tsp Ground ginger
- ⅛ tsp Ground cloves
- ½ tsp Baking soda
- 1 tsp Baking powder
- ¼ tsp Salt
- ¼ cup Chopped walnuts or pecans (optional)
- ¼ cup Dark chocolate chips (optional)
- 1½ cups Whole wheat flour
Oats and Cinnamon Sugar Crumble Topping
- ¼ cup Rolled oats
- 2 tbsp Brown sugar or coconut sugar
- ½ tsp Ground cinnamon
- 1 tbsp Melted butter or coconut oil
- Pinch of salt (optional)
Instructions
- Preheat oven to 350°F (175°C) and line a muffin tin with paper liners or lightly grease with oil.
- In a large bowl, whisk together the pumpkin puree, eggs, maple syrup (or honey), melted coconut oil, almond milk, and vanilla extract until smooth.
- Add the ground cinnamon, nutmeg, ginger, cloves, extra cinnamon, baking soda, baking powder, and salt. Stir until fully combined.
- Fold in the whole wheat flour.
- If desired, fold in the chopped nuts and/or dark chocolate chips.
- Divide the batter evenly among the muffin cups, filling each about 3/4 full.
- Bake for 18-22 minutes, or until a toothpick inserted in the center comes out clean.
- Let the muffins cool in the pan for 5 minutes, then transfer them to a wire rack to cool completely.
Instructions for Oats and Cinnamon Sugar Crumble Topping
- In a small bowl, combine the oats, brown sugar, cinnamon, and a pinch of salt (if using).
- Pour in the melted butter or coconut oil and mix until the ingredients are fully coated and crumbly.
- Sprinkle the mixture evenly over the muffin batter before baking.
- Bake the muffins as directed, and the crumble will create a sweet, crunchy topping.
Notes
- At Room Temperature: Store the muffins in an airtight container for up to 3 days. Make sure they are fully cooled before storing to avoid moisture buildup.
- In the Refrigerator: If you want them to last a bit longer, place the muffins in an airtight container and refrigerate for up to a week. You can warm them slightly before eating.
- Freezing: For longer storage, wrap the muffins individually in plastic wrap and place them in a freezer-safe bag. They can be frozen for up to 3 months. Thaw them at room temperature or pop them in the microwave for a quick warm-up.
Conclusion
There’s nothing better than a batch of homemade pumpkin chocolate chip muffins to welcome the cozy fall season. They’re easy to make and flavorful, making them perfect for busy mornings or a sweet afternoon treat with a cup of coffee. Plus, knowing they’re a healthier option makes enjoying them even better. Give them a try, and I’m sure they’ll quickly become a go-to recipe in your kitchen.
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Great recipe! I don’t think I’ve ever had anything sweet with pumpkin before so I’ll definitely need to give these ones a try (I don’t think it’s very common down under to get sweet pumpkin dishes). Love muffins! – Ash 🙂
That’s very interesting. These pumpkin chocolate chip muffins are not overly sweet but do satisfy a sweet tooth.
These look delicious!
Thank you, Ashlee!
I love the homemade pumpkin spice mix touch in these muffins! There is so much more flavour when you do it with fresh spices—it takes those muffins to another level!
I totally agree! Fresh fall spices are a must this time of year!
Yum! Will have to try these.
Let me know what you think 🙂
Yummy! I love that you used simple, whole ingredients! That’s definitely right up my alley! Thanks for sharing!
Thank you, Katie! While I love a traditional recipe, I’m trying to focus more on healthier, yet still delicious options.
These look amazing!! Love pumpkin anything at this point haha
Hahaha! Thank you! Tis the season for all things pumpkin!
These look so delicious, thanks for sharing this recipe!
My pleasure!
My family loves muffins and we are always on the lookout for new recipes to try. This one looks delicious and simple to make.
These are very easy to make and sure to be a crowd-pleaser this fall 🙂
These look really good. I saved this so I can try them. I love everything pumpkin!
Let me know how you like them 🙂
Wowowow, its looks really appetising! A fun recipe to try out for the season
These pumpkin chocolate chip muffins are so good and made with healthier ingredients. A definite win-win!
These look like the perfect recipe to get ready for fall!
Very much so! 🙂
These look absolutely delish !
Thank you 🙂
Ooo! this looks delish! I can’t wait to try this out! Thanks for the recipe
They were a big hit with my family! I do hope you enjoy them as much as they did!!
Thank you for the great instructions on how to make Pumpkin Chocolate Chip Muffins. I love that the recipe is both healthy and flavorful for a delicious fall treat.
Thank you for the great instructions on how to make Pumpkin Chocolate Chip Muffins. I love that the recipe is both healthy and flavorful for a delicious fall treat.
My pleasure! I’m always up for a healthier alternative to a decadent treat.
Look very good 👍
Thank you 🙂