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    Home » Recipes

    Whole Grain Pumpkin Muffins

    October 19, 2021 by Stephen & Elise Compston, RD, LDs 20 Comments

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    Tender, moist, and perfectly spiced, these Whole Grain Pumpkin Muffins are a family favorite! Enjoy this simple recipe year round.

    Overhead shot of Whole Grain Pumpkin Muffins

    Poor pumpkins. 8 months out of the year they are ignored, overlooked, and practically forgotten. Then fall rolls around and WABAM! Pumpkin. Overload. From PSLs to pumpkin spiced pumpkin seeds (yes, that’s a thing) we can’t seem to escape pumpkin mania. Unfortunately, most “pumpkin” flavored treats are loaded with added sugar and rarely contain any real pumpkin at all! It's a shame, because real pumpkin contains good-for-you nutrients that should be enjoyed year round! From soups, to smoothies, to bread, to pasta sauces, there are so many ways to love it.

    Today we're sharing our family recipe for Whole Grain Pumpkin Muffins. Made with nutrient-rich whole wheat flour, just the right touch of sweetness, and 2 CUPS of real pumpkin, these are muffins you can feel good about enjoying any time of year. These muffins go FAST in our house which is why we usually make two batches at a time! They freeze well and make perfect additions to lunchboxes for your littles. We are so excited for you to try them!

    RECIPE NOTES

    Flour. We most often reach for whole wheat pastry flour or white whole wheat flour for our baked goods. Both are rich in whole grain nutrients but mild in color, flavor, and texture which makes them great for baking. If looking for a gluten friendly alternative, we love Trader Joe's Gluten Free All Purpose Flour or this Bob's Red Mill 1-1 baking flour.

    Overhead shot of Whole Grain Pumpkin Muffin ingredients
    These muffins are made with TWO whole cups of pumpkin!

    Oil. We have made these muffins with everything from walnut, to coconut, to olive oil with great success. Use your favorite! Subbing with butter? Increase to 1 cup softened.

    Baking Tray. We are BIG fans of silicone baking trays. They are non-stick, safe, and make light work of extracting muffins. Our favorite brand is Trudeau, which makes a line of silicone bakeware. No greasing, muffin liners, or scrubbing required!

    HOW TO MAKE

    Step 1
    To make, start by combining the your dry ingredients, followed by wet ingredients, in two separate mixing bowls.

    Overhead shot of a two bowls; of wet ingredients and dry muffin ingredients

    Step 2
    Once prepared, combine wet and dry ingredients and fold to combine, careful not to over mix.

    Closeup shot of wet muffin ingredients being added to dry.
    The key to soft, fluffy muffins is folding the ingredients together just enough to mix. Over stirring can cause muffins to become dense.

    Step 3
    Next, add 1 scoop of batter to each muffin tin, followed by a sprinkle of chocolate chips.

    Image of muffin batter being scoop into a muffin tray

    Repeat step 3, adding a second layer of batter and chocolate chips to your muffins.

    Overhead shot of Whole Grain Pumpkin Muffins in a tray before baking

    Step 4
    Bake until golden and fluffy!

    Overhead shot of baked pumpkin muffins and loaf
    This recipe makes roughly 18-20 muffins. We fill a muffin tray and then make a small loaf in another pan!
    Overhead shot of Whole Grain Pumpkin Muffins
    Print Recipe
    5 from 16 votes

    Whole Grain Pumpkin Muffins

    Tender, moist, and perfectly sweet, these Whole Grain Pumpkin Muffins are a family favorite! This simple recipe can be enjoyed year round.
    Prep Time15 mins
    Cook Time25 mins
    Total Time40 mins
    Course: Dessert, Snack
    Cuisine: American
    Servings: 18 muffins
    Calories: 165kcal

    Ingredients

    • 2 cups Whole Wheat Pastry Flour can sub with all-purpose or GF
    • 2 ¼ teaspoon ground cinnamon
    • ¾ teaspoon ground ginger
    • ⅛ tsp ground allspice
    • 1 teaspoon baking soda
    • ½ teaspoon baking powder
    • ½ teaspoon salt
    • ¾ cup packed brown sugar
    • ¾ cup avocado oil
    • 3 eggs
    • 2 teaspoon vanilla extract
    • 2 cups pumpkin puree canned or freshly roasted
    • ½ cup chocolate chips, walnuts, or other add-ins

    Instructions

    • Preheat oven to 350°F.
    • In a large mixing bowl, combine flour, spices, baking soda, baking powder, and salt. Stir to combine and set aside.
    • In another bowl, combine brown sugar, pumpkin, oil, vanilla, and eggs. Add wet mixture to dry and stir until JUST combined. A few lumps are ok but be careful not to overmix.
    • Using a melon baller or tablespoon, scoop a spoonful of batter into each tin. Sprinkle a few chocolate chips or other favroite add-ins into each cup. Finish off by adding another spoonful of batter until each tin is roughly ¾ of the way full. Add a final sprinkle of chocolate.
    • Bake for 23-25 minutes, or until muffins are fluffy, golden, and pass the toothpick test. Let sit for 10 minutes prior to transferring to a wire rack to cool.

    Notes

    This recipe yields roughly 18-20 muffins. We often bake 1 tray of muffins and make a small loaf in a glass baking dish which can easily be frozen to be enjoyed at a later date. 

    Nutrition

    Calories: 165kcal

    Looking for more muffin inspiration? Check out our made-for-summer Strawberry Ricotta Muffins and fan favorite and No Sugar Added Banana Hemp Muffins.

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    Reader Interactions

    Comments

    1. John Garris

      November 15, 2022 at 11:42 am

      5 stars
      I really like pumpkin bread so I will definitely have to give these a try!

      Reply
      • Stephen & Elise Compston, RD, LDs

        November 20, 2022 at 9:24 am

        Hi John, we hope you enjoy them!

        Reply
      • Stephen & Elise Compston, RD, LDs

        November 20, 2022 at 9:55 am

        Hi John, we hope you love them!

        Reply
    2. Margo

      November 08, 2022 at 1:50 pm

      5 stars
      I have a sweet tooth and with it being fall season, I think these muffins would make the perfect treat to try with family or friends. I plan to give this recipe a try.

      Reply
      • Stephen & Elise Compston, RD, LDs

        November 20, 2022 at 9:35 am

        Hi Margo, we hope you enjoy!

        Reply
    3. Lilly Carroll

      October 27, 2022 at 12:56 pm

      5 stars
      I made these for me and my roommates with gluten free flour and they were amazing! Definitely will be making them for my family over break, the perfect way to get in the fall spirit!

      Reply
      • Stephen & Elise Compston, RD, LDs

        November 20, 2022 at 9:52 am

        Hi Lily, so glad to hear the muffins were a hit! Thanks so much for the feedback.

        Reply
    4. Margo Norwood

      October 16, 2022 at 6:23 pm

      I have a sweet tooth and with fall season rolling in, I think these muffins would make the perfect treat to try with family or friends! I plan to give this recipe a try.

      Reply
    5. maddie barfield

      October 06, 2022 at 12:16 pm

      5 stars
      These muffins look delicious! They seem perfect for fall and easy enough to make. I will definitely try this recipe soon!

      Reply
    6. Rachel Kelley

      September 08, 2022 at 2:44 pm

      5 stars
      I made this last night and it super easy to do and really good!
      - Rachel Kelley

      Reply
    7. Sophia Wagner

      August 26, 2022 at 10:56 am

      5 stars
      I am a sucker for anything pumpkin so these seem so hearty and delicious! Will definitely have to try.

      Reply
      • Stephen & Elise Compston, RD, LDs

        August 30, 2022 at 12:08 pm

        Hi Sophie, thank you so much! We hope you love them!

        Reply
    8. Maren Mckean

      August 26, 2022 at 8:31 am

      5 stars
      Looks so good!!
      -Maren Mckean

      Reply
      • Stephen & Elise Compston, RD, LDs

        August 26, 2022 at 8:49 am

        Thank you so much! We hope you enjoy!

        Reply
    9. Marissa La Venuta

      August 26, 2022 at 8:18 am

      5 stars
      I am always looking for healthier options and an easy bake. These were great!

      Reply
      • Stephen & Elise Compston, RD, LDs

        August 26, 2022 at 8:23 am

        Hi Marissa, so glad you enjoyed them! Thanks for the feedback.

        Reply
    10. Judy

      December 27, 2021 at 8:13 pm

      5 stars
      These fit the bill! Thank you.

      Reply
      • Stephen & Elise Compston, RD, LDs

        January 24, 2022 at 4:01 pm

        So glad you enjoyed them!

        Reply
    11. Amanda

      October 23, 2021 at 12:49 pm

      5 stars
      Delicious! Just enough sweetness and my two toddlers who will turn their nose up at anything pumpkin enjoyed them very much (the chocolate chips won them over😊). Thanks for this recipe!

      Reply
      • Stephen & Elise Compston, RD, LDs

        October 24, 2021 at 2:09 pm

        Hi Amanda, we are SO happy to hear that the muffins were a hit with all members of your family. Thank you for trying them out and letting us know what you thought!

        Reply

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    The Compstons

    We're Stephen and Elise Compston! Husband and wife registered dietitians, recipe revitalizers, and developers of upgraded everyday eats. We create simple, affordable, plant-focused recipes with fun, fresh, and creative spins on classic dishes and tasty new favorites.

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