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Pumpkin Chocolate Chip Whole Wheat Muffins

Pumpkin Chocolate Chip Whole Wheat Muffins

This is definitely a fall-time favourite dessert recipe to make as the weather cools down and the leaves begin to change colour. I can’t wait because autumn is my favourite season. One more month… I like summer, but the heat and me don’t always agree.

These muffins are perfect for fall or autumn (what do you like to call this season?) where all things pumpkin are in season! This includes my One-Pot Spaghetti with Creamy Pumpkin Sauce!

This recipe features pumpkin puree, cinnamon, and sweet chocolate chips giving them a wonderful combination of flavours.

Bowls of chocolate chips, sugar, oil, pumpkin puree, baking soda, baking powder, spices,and eggs.

All the ingredients are measured out and ready to be combined.Amounts can be found in the “Ingredients” list below.

Pumpkin chocolate chip whole wheat muffin batter in a glass bowl with a metal whisk.

The batter is mixed up and ready to placed in the muffin pan.

Pumpkin chocolate chip whole wheat muffin batter scooped evenly into a 12 cup muffin pan.

Bake at 400 degrees F for 12-15 minutes and you’ve got some scrumptious muffins!

Pumpkin chocolate chip whole wheat muffins placed on a rectangular wooden board and on a white plate.

I love baking with pumpkin puree because not only it gives the muffins a mild pumpkin flavour and a nice orange colour, but it also helps keep the muffins soft and moist.

Also,remember that pumpkin puree is made from pure pumpkin and is not the same as pumpkin pie filling.

Pumpkin pie filling is usually already spiced and sweetened and you don’t want a muffin that’s too sweet and overly spiced. Using puree, you can play around with different spices and sweetness levels to suit your own tastes.

Close-up shot of a pumpkin chocolate chip whole wheat muffin with a big bite taken out of it with muffins in the background.

I decided to switch out regular all-purpose flour for whole wheat flour to give the muffins a slight wheat flavour, a little more texture and bulk, but fortunately, the end result will not be dense. The muffins will turn out fluffy and tender.

Also, whole wheat flour has more fiber, protein, iron, calcium, and other nutrients than white flour, which is a plus in my books.

Finally, the chocolate chips bring it all together. I tend to gravitate towards using semi-sweet chocolate chips for baking (and occasional snacking) since they have a rich, dark chocolatey flavour compared to milk chocolate. If you prefer a more sweeter and milky flavour, you can always go with milk chocolate chips.

No electric mixer is required for this one. Just a whisk or a spatula and a couple of bowls will do the trick before baking them up in a muffin pan. Easy to assemble and the clean-up is pretty minimal too.

I hope you enjoy this recipe!

A top angled view of three pumpkin chocolate chip whole wheat muffins, one that is half-eaten, on a white plate.
Pumpkin Chocolate Chip Whole Wheat Muffins

Pumpkin Chocolate Chip Whole Wheat Muffins

Yield: 18 muffins
Prep Time: 15 minutes
Cook Time: 15 minutes
Total Time: 30 minutes

A tasty dessert that’s perfect for fall! Delicious, soft, and full of chocolate chips, these pumpkin muffins are easy to make and ready in 30 minutes!


  • 1½ cups whole wheat flour
  • 1 tsp baking soda
  • 1 tsp baking powder
  • 1 tsp ground cinnamon
  • ¼ tsp salt
  • 1½ cups pumpkin puree
  • 1 cup vegetable (cooking) oil
  • ½ cup brown sugar, packed
  • ¼ cup white sugar
  • 2 eggs
  • 1 ¼ cup chocolate chips (I used semi-sweet)


  1. Preheat the oven to 400 degrees F. Line a large muffin pan with baking cups (liners).
  2. In a large bowl, whisk together the flour, baking soda, baking powder, cinnamon, and salt until well combined. Set aside.
  3. In another bowl, whisk together the pumpkin puree, oil, sugars, and eggs until well incorporated. Then, pour the pumpkin puree mixture into the flour mixture and stir until combined and the batter is smooth.
  4. Then, gently fold 1 cup of chocolate chips into the batter, reserving ¼ cup of chocolate chips. Scoop the batter into each muffin pan cup about ⅔ full. Top each muffin with the reserved chocolate chips.
  5. Bake for 12-15 minutes until a wooden skewer (or cake tester) comes out clean in the center. Let cool slightly before eating.


  • To store muffins 2-4 days: Completely cool the muffins, line an airtight storage container or a large Ziploc bag with a paper towel, place the muffins in a single layer, and then top with another paper towel before sealing. Store the bag at room temperature.
  • To store muffins for longer than 4 days: Completely cool the muffins, wrap each muffin with plastic wrap or aluminum foil, and place in a freezer bag before freezing. Thaw at room temperature or reheat in the microwave before eating.

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Nutrition Information:
Yield: 18 Serving Size: 1
Amount Per Serving: Calories: 234Total Fat: 16gCarbohydrates: 23.8gProtein: 2.6g

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Tuesday 26th of November 2019

I’m making these tomorrow for Thanksgiving and my son’s birthday, that happens to fall on Thanksgiving this year. Can’t wait!!! I want to make some small bite size muffins. How much time do you suggest in the oven for small muffins??

Marie | Yay! for Food

Tuesday 26th of November 2019

Hi Julianna! I've never tried making these muffins into mini muffins before so I can't tell you baking times with exact centainty. I suggest that you make a "test" mini muffin (or two) to bake and start checking them after 7 minutes (and every minute after) until it is fully baked (noting how long it takes). After, you can make a full batch. I hope this helps. Happy Thanksgiving and Happy Birthday to your son too!

Nicoletta @sugarlovespices

Wednesday 6th of September 2017

Simply love them! I hardly ever have any pumpkin puree at home, and that might change soon ;-) !

Marie | Yay! For Food

Wednesday 6th of September 2017

My house is all pumpkin spice and pumpkin puree all fall long! :) I hope you try some pumpkin treats soon.

Linda @ 2 Cookin Mamas

Wednesday 6th of September 2017

Such beautiful pictures! I love the idea of using whole wheat flour along with the pumpkin. And chocolate chips are always necessary. :-)

Marie | Yay! For Food

Wednesday 6th of September 2017

Yes of course! ;) Thanks Linda!


Tuesday 5th of September 2017

I can see you love your pumpkin Marie! So many great pumpkin recipe. This looks amazing! I'm pinning this :D

Marie | Yay! For Food

Wednesday 6th of September 2017

Thanks for pinning! :)

GiGi Eats

Sunday 27th of August 2017

UGhhh I could totally eat 5 of those and still want more!

Marie | Yay! For Food

Sunday 27th of August 2017

I love these muffins! :) Thanks for stopping by!

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