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Home » Recipe Index » Loaves, Muffins and Scones

Whole Wheat Pumpkin Chocolate Chip Muffins

Published: Oct 24, 2015 · Modified: Jan 29, 2025 by Fida | Sweet and Savoury Pursuits · This post may contain affiliate links · 16 Comments

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These Whole Wheat Pumpkin Chocolate Chip Muffins are a delicious, wholesome treat the whole family will enjoy!

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

Autumn is in full swing here and the trees are beautiful with golden and crimson leaves. This seasons also means that bakeries and coffee shops are filled with baked pumpkin treats and pumpkin spiced lattes, something that I look forward to every year.

Pumpkin Chocolate Chip Muffin cut in half with more muffins in the background.
Jump to:
  • Whole Wheat Pumpkin Muffins
  • Tips
  • Storage Instructions
  • More Squash Recipes
  • Whole Wheat Pumpkin Chocolate Chip Muffins Recipe

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.

To make something the kids would love, I used chocolate chips instead of nuts for pumpkin muffins that are truly kid-friendly. The combination of pumpkin and chocolate isn't only delicious in these muffins, it's also fabulous in this Chocolate Swirl Pumpkin Loaf and in this Pumpkin Chocolate Swirl Bundt Cake!

Whole Wheat Pumpkin Muffins

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

The pumpkin purée makes these muffins very moist and they will stay that way for days. Though these squash muffins are made with whole wheat pastry flour, they are just as tender, fluffy and delicious as muffins made with all-purpose flour.

Tips

  • I also like using mini chocolate chips instead of 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 spice muffins in a mini muffin tin.
Whole Wheat Pumpkin Chocolate Chip Muffins on board with basket of muffins in the background.

Storage Instructions

Once the pumpkin 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 love baked pumpkin treats, give this pumpkin bread recipe a try. It's one of my favorites. The bread is made with walnuts but you can use chocolate chips for a recipe your kids will love.

More Squash Recipes

  • Pumpkin Scones with Espresso Glaze
  • Pumpkin Chocolate Swirl Bundt Cake
  • Chocolate Swirled Brown Sugar Pumpkin Loaf
  • Butternut Squash and White Bean Dip
  • Roasted Butternut Squash and Pear Soup
Pumpkin chocolate chip muffins on wood board.

Whole Wheat Pumpkin Chocolate Chip Muffins Recipe

Author: Sweet and Savoury Pursuits
These Whole Wheat Pumpkin Chocolate Chip Muffins are a delicious, wholesome treat the whole family will enjoy!
4.67 from 9 votes
Print Recipe Pin Recipe Save Saved!
Prep Time 20 minutes mins
Cook Time 20 minutes mins
Total Time 40 minutes mins
Course Breakfast, Snack
Cuisine American
Servings 12 muffins
Calories 237 kcal

Ingredients
  

  • 1-½ cups whole wheat pastry flour
  • 1 teaspoon ground cinnamon
  • 1 teaspoon baking soda
  • ½ teaspoon baking powder
  • ½ teaspoon sea salt
  • ½ teaspoon ginger
  • ¼ teaspoon ground nutmeg
  • ⅛ teaspoon ground cloves optional
  • 2 large eggs
  • ½ cup granulated sugar
  • ½ cup packed light brown sugar
  • 1-¼ cups pumpkin puree canned
  • ½ cup light olive oil or canola oil
  • ½ cup semi-sweet mini chocolate chips plus 1 Tbsp. for sprinkling on top before baking

Instructions
 

  • 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.

Nutrition

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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Comments

    4.67 from 9 votes (9 ratings without comment)

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  1. Abida says

    November 07, 2015 at 1:05 pm

    I'm not quite ready to give up gluten in my desserts so I think whole wheat muffins would make a great healthier option for baking, sounds great!

    Reply
  2. chewtown says

    October 25, 2015 at 10:40 pm

    Thanks to the worldwide pumpkin shortage, pumpkins in Australia are beyond expensive... but the moment they are more affordable, I'm definitely making these. Love the addition of chocolate chips for a little treat.

    Reply
    • Sweet and Savoury Pursuits says

      October 26, 2015 at 5:29 pm

      I know I heard about it recently on the news, hopefully next year will be better for pumpkin growers. I guess I was lucky to have bought my canned pumpkin early in the season! Thanks for stopping bye 🙂

      Reply
  3. Jessica @ Sweetest Menu says

    October 25, 2015 at 6:08 pm

    These look gorgeous! Totally pinning right now!

    Reply
    • Sweet and Savoury Pursuits says

      October 25, 2015 at 7:59 pm

      Thanks Jessica, it's the mini chocolate chips they make everything look great!

      Reply
  4. C.M. says

    October 25, 2015 at 10:40 am

    Delicious looking muffins, love everything pumpkin!

    Reply
    • Sweet and Savoury Pursuits says

      October 25, 2015 at 10:47 am

      Thanks so much!

      Reply
  5. Lynz Real Cooking says

    October 24, 2015 at 3:59 pm

    These look amazing!

    Reply
    • Sweet and Savoury Pursuits says

      October 25, 2015 at 10:49 am

      Thank you so much Lynz. Hope you have a great rest of the weekend!

      Reply
      • Lynz Real Cooking says

        October 25, 2015 at 10:52 am

        Thanks you too!

        Reply
        • Sweet and Savoury Pursuits says

          October 25, 2015 at 10:52 am

          Thanks!

          Reply
  6. Alex says

    October 24, 2015 at 3:49 pm

    These look great, nice pictures.

    Reply
    • Sweet and Savoury Pursuits says

      October 24, 2015 at 5:27 pm

      Thanks Alex!

      Reply
  7. nancyc says

    October 24, 2015 at 12:10 pm

    Yum! These sound like great muffins for this time of year!

    Reply
    • Sweet and Savoury Pursuits says

      October 25, 2015 at 10:37 am

      Thanks Nancy, I think so too 🙂

      Reply
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