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Whole Wheat Pumpkin Chocolate Chip Muffins

Treat yourself and your family by making a batch of these delicious, easy, moist and tender, kid-friendly Whole Wheat Pumpkin Chocolate Chip Muffins.

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Three Pumpkin Chocolate Chip Muffins on a board with a basket of muffins in the background.

Autumn is in full swing here, the trees are beautiful with golden and crimson leaves. I will never tire of seeing summer transition into fall, it's quite a spectacular scene.

Fall also means that bakeries and coffee shops are filled with baked pumpkin goods and pumpkin spiced lattes. And that's just fine by me, as I always look forward to having my first pumpkin latte of the season and love baked pumpkin goodies.

Pumpkin Chocolate Chip Muffin cut in half with more muffins in the background.

Kid-Friendly Pumpkin Muffins

When I think of baked pumpkin goods I usually think of them with nuts or pumpkin seeds in them. I love having that element of crunch in a slice of pumpkin loaf or a muffin.

But this time I wanted to bake something the kids would really enjoy and sadly mine don't feel the same way I do about nuts in baked goods 🙁. So this time I added chocolate chips to the recipe for pumpkin muffins that are kid-friendly!

The combination of pumpkin and chocolate is delicious, and my kids just love these Whole Wheat Pumpkin Chocolate Chip Muffins!

Whole Wheat Pumpkin Chocolate Chip Muffins on board with basket of muffins in the background.

Whole Wheat Pumpkin Muffins

The muffins are spiced perfectly with the combination of cinnamon, nutmeg, ginger and cloves, a classic combination of flavours that complement pumpkin so well.

The pumpkin purée makes these muffins very moist and they will stay that way for days. Using whole wheat pastry flour makes them healthier for you without reducing the tenderness, fluffiness or taste of the muffins.

I also like using mini chocolate chips instead of the regular-sized in my muffin recipes because they distribute better. But you can use whichever you prefer or have on hand.

Adding a few chocolate chips to the top of the muffins before baking them will make the muffins look extra chocolatey and make the kids extra happy 😀.

For toddler sized muffins, you can bake these pumpkin muffins in a mini muffin tin.

How to Store Muffins

Once the muffins have cooled completely, store them in an airtight container with paper towels at the bottom and top of the muffins. Paper towels will absorb the extra moisture from the muffins and keep them fresh for longer.

You can also freeze extra muffins to keep them fresh for longer than four days. Transfer the airtight container to the freezer or place muffins in a freezer bag. Muffins can be frozen for up to three months.

Defrost overnight in the refrigerator and warm slightly in a low-temperature oven. For more information on storing quick breads and muffins, check out this post from TheKitchn.

If you're a lover of baked pumpkin goods you should try this pumpkin bread recipe. It's one of my favourite pumpkin recipes. The bread is made with walnuts but you can use chocolate chips for another recipe your kids will love.

More Squash Recipes

Three Pumpkin Chocolate Chip Muffins on a board with a basket of muffins in the background.

Whole Wheat Pumpkin Chocolate Chip Muffins

Sweet and Savoury Pursuits
Bake these tender and moist Whole Wheat Pumpkin Chocolate Chip Muffins to experience the delicious combination of pumpkin and chocolate.
4.67 from 6 votes
Prep Time 20 mins
Cook Time 20 mins
Total Time 40 mins
Course Breakfast, Snack
Cuisine American
Servings 12 muffins
Calories 237 kcal


  • 1-1/2 cups whole wheat pastry flour
  • 1 tsp. baking soda
  • 1/2 tsp. baking powder
  • 1/2 tsp. sea salt
  • 1 tsp. ground cinnamon
  • 1/2 tsp. ginger
  • 1/4 tsp. ground nutmeg
  • 1/8 tsp. ground cloves optional
  • 2 large eggs
  • 1/2 cup granulated sugar
  • 1/2 cup packed light brown sugar
  • 1-1/4 cups pumpkin puree canned
  • 1/2 cup light olive oil or canola oil
  • 1/2 cup semi-sweet mini chocolate chips plus 1 Tbsp. for sprinkling on top before baking


  • Position a rack in the center of the oven and heat the oven to 350°F.
  • Line a muffin pan with 12 paper cups.
  • In a medium bowl, whisk together the flour, baking soda, baking powder, salt, cinnamon, ginger, nutmeg and cloves (if using). Set aside.
  • In a medium bowl, whisk together the sugars, eggs and oil until well combined.
  • Add in the pumpkin purée and blend well.
  • Add the wet ingredients into the dry and mix using a rubber spatula, do not over-mix the batter, it's fine to have a few lumps.
  • Add the chocolate chips and using the rubber spatula fold into the batter
  • Divide batter between the 12 muffin cups, they should be full.
  • Bake for 18 to 20 minutes, or until a toothpick inserted into the center comes out clean.
  • Let muffins cool in the pan for a few minutes then remove from muffin pan and place onto rack to cool completely.


Calories: 237kcalCarbohydrates: 27gProtein: 2gFat: 13gSaturated Fat: 3gCholesterol: 27mgSodium: 206mgPotassium: 127mgFiber: 1gSugar: 21gVitamin A: 840IUVitamin C: 0.2mgCalcium: 34mgIron: 1.1mg
Keyword Pumpkin Chocolate Chip Muffins, Pumpkin Muffins, Whole Wheat Pumpkin Chocolate Chip Muffins
Tried this recipe? Have any questions, comments or suggestions? Leave a comment below!Mention @sweetandsavourypursuits or tag #sweetandsavourypursuits!


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