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    Home » Recipes » Muffins and Breads

    Healthy Chocolate Pumpkin Muffins

    UPDATED Oct 17, 2019 · PUBLISHED Oct 15, 2019 BY Marjory Pilley · This post may contain affiliate links. As an Amazon Associate I earn from qualifying purchases.

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    Healthy Chocolate Pumpkin Muffins Pin

    Healthy Chocolate Pumpkin Muffins are a must-have for fall! And, you don't have to resist either. They're made with whole wheat flour, Greek yogurt, cocoa powder, and lots of pumpkin and are absolutely irresistible!

    Close-up of healthy chocolate pumpkin muffin with 2 muffins and pumpkin in the background.

    We "chocolatized" Greek yogurt pumpkin muffins, one of our most popular Fall Recipes. Because chocolate makes everything better! Are you with me? 🙂

    In this case, chocolate does NOT mean unhealthy. We used our master muffin mix with Greek yogurt, whole wheat pastry flour, and less refined sugar. They're naturally packed with extra protein so they're anytime muffins...as in you can have them for a snack, dessert, or even breakfast!

    Ingredients in Healthy Chocolate Pumpkin Muffins

    As we always say, healthy means something different to everyone. With that in mind, here are the key ingredient swaps we made from a traditional muffin recipe and a few other substitutions we've tried.

    • Whole wheat pastry flour is our go-to flour for all of our Bread and Muffin Recipes.
      • Why do we like this type of flour?
        • The entire wheat berry is ground (germ, bran and all) just like whole wheat flour. But, a "soft" wheat berry is used instead of the "hard" one used in whole wheat flour. Whole wheat pastry flour is finely ground so it's lower in protein and gluten. It has a mild flavor and works well with baked goods.
      • Other Options:
        • White whole wheat flour
        • 100% whole wheat flour
        • A mixture of whole wheat and all-purpose flour (try ½ and ½)
        • Unbleached all-purpose flour
    • Greek Yogurt replaces the oil that is often used in muffin recipes. It typically comes in a 5.3 ounce container. Scrape it all in. No measuring required.
      • Oil can be used instead. Watch the batter consistency and possibly use less milk.
    • Unsweetened Cocoa Powder. Even better, try unsweetened dark chocolate cocoa powder!
    • Milk gets the batter for these chocolate pumpkin muffins to the right consistency. Most any milk will work, including almond milk. We used skim in the muffins pictured.
    • Dark Chocolate Chips adds more chocolate flavor. You know how it goes, the darker the better. Of course, any chip will work. If you can find them, use mini chocolate chips to more easily distribute through all the muffins.
    • Sugar! We used a ½ cup of sugar. That's not much distributed across 16 muffins in my book. It works out to be 1.5 teaspoons per muffin. We've used stevia/sugar blends before and they will work. So, if that's what you normally use for baking, go ahead and substitute it according to the directions for the replacement.
    • Egg - One egg or egg-replacer will work in this recipe.
    • Pumpkin puree from a can (that's what we used) or check out How to Make Pumpkin Puree by Jessica Gavin.
    • Salt, baking powder, baking soda, cinnamon, and vanilla round out the ingredient list.

    If you're looking for a gluten-free version, then check out Healthy Oatmeal Pumpkin Muffins which could easily receive the same makeover!

    Three Healthy Chocolate Pumpkin Muffins in front of a pumpkin

    See How We Made Chocolate Pumpkin Muffins

    Once the recipe ingredients are gathered, these healthy chocolate pumpkin muffins are a breeze to make!

    First mix the dry ingredients together: flour, sugar, cocoa powder, salt, baking powder, baking soda, and cinnamon.

    Measuring cup with cocoa powder being emptied into mixing bowl for chocolate pumpkin muffins

    Next, add the wet ingredients: pumpkin puree, Greek yogurt, vanilla extract, egg, and milk. Stir until well-combined. The batter should be thick enough to stick to a spoon for a few seconds.

    Healthy Chocolate Pumpkin Muffin batter on a spoon over a mixing bowl.

    Fold in chocolate chips. We used 60% cacao dark chocolate chips.

    Dark Chocolate Chips in measuring cup over chocolate pumpkin batter.

    Use paper inserts or don't. Either way, spray the muffin pan with non-stick cooking spray. Fill the wells about ⅔ full of batter. An ice cream scoop with a lever makes quick work of this task.

    Ice cream scoop putting chocolate pumpkin muffin batter in cupcake baking pan.

    Bake healthy chocolate pumpkin muffins in a 350 degree Fahrenheit oven for about 25 minutes or until the top is firm.

    Overhead shot of the best chocolate pumpkin muffins with 2 pumpkins on a brown paper bag

    Allow them to cool in the pan for 5-10 minutes and then ENJOY!

    Expert Tips for the BEST Chocolate Pumpkin Muffins

    1. IF you use a different flour, then you MAY need to adjust the milk accordingly. Start with a small increment, like 1 teaspoon.
      • Add a little extra milk if using 100% whole wheat flour.
      • Start with a quarter cup of milk if using regular pastry flour and add the remaining milk back as needed.
      • The batter should be thick and stick to a spoon for a few seconds. (See the picture above.)
    2. Spray the cupcake tin with non-stick cooking spray. If you're using paper inserts spray the inside of those too! Otherwise, the muffins will stick to the pan because there is no oil!
    3. Did you forget to spray the well? Eventually, the moisture will settle and it will be easier to remove the paper liner...if you can wait!
    4. Sift the cocoa powder to remove the tiny clumps before you measure it out!
    5. Gently spoon the flour into the measuring cups. I don't sift the flour (although it's not a bad idea.) You don't want to "pack" it or the batter will be too thick.
    6. Use an ice cream scoop with a quick release to easily and consistently dish out the batter. We used a blue thumb presser that measures a quarter cup.
    7. Allow muffins to cool in the tin for 5-10 minutes.
    8. Make an extra batch of the dry ingredients and store in a tightly sealed jar so the muffins are even easier to make the next time.
    9. Store chocolate pumpkin muffins in an airtight container for 2-3 days. Or, store in the freezer for about 2 months.

    Chocolate Pumpkin Muffins with chocolate chips piled on a plate.

    They are sure to be a winner with friends and family!

    Please rate this recipe and tag @DinnerMom or #DinnerMom on social media. We love to see what you are cooking up!

    Close-up of healthy chocolate pumpkin muffin with 2 muffins and pumpkin in the background.

    Healthy Chocolate Pumpkin Muffins

    No need to resist these Healthy Chocolate Pumpkin Muffins made with whole wheat flour, Greek yogurt, and cocoa. Eat them for a snack, dessert or breakfast!
    4.20 from 5 votes
    Print Pin Rate
    Course: Snack
    Cuisine: American
    Prep Time: 15 minutes
    Cook Time: 25 minutes
    Total Time: 40 minutes
    Servings: 14 Muffins
    Calories: 131kcal
    Author: Marjory Pilley

    Ingredients

    • 1½ cup whole wheat pastry flour
    • ¼ cup unsweetened cocoa powder
    • ½ cup sugar
    • ½ teaspoon baking powder
    • ½ teaspoon baking soda
    • ½ teaspoon salt
    • ½ teaspoon ground cinnamon
    • 15 ounce pumpkin puree
    • 1 teaspoon vanilla extract
    • ⅓ cup skim milk
    • 1 egg beaten
    • 5.3 ounce non-fat Greek yogurt
    • ½ cup chocolate chips preferably dark

    Instructions

    • Preheat oven to 350 degrees F.
    • Combine flour, cocoa powder, sugar, baking powder, baking soda, salt and cinnamon in a bowl.
    • Stir pumpkin, vanilla extract, milk, egg and Greek yogurt into the dry mix.
    • Fold in mini chocolate chips.
    • Fill muffins tins lined with paper liners or coated with cooking spray about ⅔ full. (Tip: if using liners, give them a light spritz of cooking spray before filling them with batter.)
    • Bake for 20-25 minutes or until firm.
    • Allow muffins to cool for 5 minutes and then remove to a wire rack to cool further.

    Notes

    SEE STEP-BY-STEP PHOTOS AND VIDEO ABOVE! 
    Expert tips:
    1. IF you use a different flour, then you MAY need to adjust the milk accordingly. Start with a small increment, like 1 teaspoon.
      • Add a little extra milk if using 100% whole wheat flour.
      • Start with a quarter cup of milk if using regular pastry flour and add the remaining milk back as needed.
      • The batter should be thick and stick to a spoon for a few seconds. (See the picture above.)
    2. Spray the cupcake tin with non-stick cooking spray. If you're using paper inserts spray the inside of those too! Otherwise, the muffins will stick to the pan because there is no oil!
    3. Did you forget to spray the well? Eventually, the moisture will settle and it will be easier to remove the paper liner...if you can wait!
    4. Sift the cocoa powder to remove the tiny clumps before you measure it out!
    5. Gently spoon the flour into the measuring cups. I don't sift the flour (although it's not a bad idea.) You don't want to "pack" it or the batter will be too thick.
    6. Use an ice cream scoop with a quick release to easily and consistently dish out the batter. We used a blue thumb presser that measures a quarter cup.
    7. Allow muffins to cool in the tin for 5-10 minutes.
    8. Make an extra batch of the dry ingredients and store in a tightly sealed jar so the muffins are even easier to make the next time.
    9. Store chocolate pumpkin muffins in an airtight container for 2-3 days. Or, store in the freezer for about 2 months.
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    Nutrition

    Calories: 131kcal | Carbohydrates: 25g | Protein: 4g | Fat: 2g | Saturated Fat: 1g | Cholesterol: 13mg | Sodium: 140mg | Potassium: 176mg | Fiber: 3g | Sugar: 13g | Vitamin A: 4770IU | Vitamin C: 1mg | Calcium: 49mg | Iron: 1mg
    Nutritional and Food Safety Disclaimer

    More Bread & Muffin Recipes

    • Healthy Oatmeal Pumpkin Muffins or "Cups" {Gluten-free}
    • Cauliflower Waffles - 3 Ingredient Chaffles!
    • Easy Keto Chaffle Recipe - Just 3 Ingredients!
    • Healthy Greek Yogurt Pumpkin Muffins
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      Recipe Rating




    1. Stephanie

      November 23, 2015 at 2:56 pm

      Wow. These look much to rich and delicious to be healthy! Good job 🙂

      Reply
    2. The Food Hunter

      November 23, 2015 at 4:01 pm

      they look absolutely irresistible!

      Reply
    3. Lauren Kelly Nutrition

      November 23, 2015 at 7:01 pm

      Chocolate + Pumpkin = Heaven! I love these ingredients, these muffins look delicious!

      Reply
    4. Lora

      November 23, 2015 at 10:22 pm

      How nice, Marjorie! It's great you used whole-wheat pastry flour. Such a great way to make decadent muffins a little bit better for you!

      Reply
    5. Renee - Kudos Kitchen

      November 24, 2015 at 8:19 am

      I love that you've added Greek yogurt into these delicious and decadent looking muffins. The look so moist and chocolaty!

      Reply
    6. Erin @ Texanerin Baking

      November 24, 2015 at 11:35 am

      I love that these are whole wheat! 🙂 And the Greek yogurt addition must be so yummy. They look nice and moist and I bet so full of flavor!

      Reply
    7. Aly ~ Cooking In Stilettos

      November 24, 2015 at 7:34 pm

      I am a huge fan of Greek yogurt in baking and these muffins need to be made for brunch this weekend. Love it!

      Reply
    8. Heather | All Roads Lead to the Kitchen

      November 24, 2015 at 9:37 pm

      I'm loving the addition of Greek yogurt, I bet it makes them so incredibly moist! Plus, chocolate and pumpkin, yes please.

      Reply
    9. Kim Beaulieu

      November 25, 2015 at 12:09 am

      I'm such a chocolate fanatic so these are calling my name. Nothing better than a big fluffy muffin in the morning. These look seriously yummy!

      Reply
    10. Kirsten/ComfortablyDomestic

      November 25, 2015 at 9:34 am

      I like to toss a few chocolate chips into my pumpkin muffins, but a chocolate pumpkin muffins sounds even more delicious! Adding yogurt to muffins gives such a great texture.

      Reply
    11. Kat

      December 04, 2015 at 11:14 am

      5 stars
      These muffins were absolute delicious. The kids and hubby couldn't even tell there was pumpkin in there - they thought I was crazy for making cupcakes for breakfast (but didn't complain about it - they just asked for seconds!) This recipe is definitely a keeper.

      Reply
      • Marjory

        December 04, 2015 at 1:20 pm

        I am so happy you enjoyed them! Thanks so much for your feedback. Made my day. 🙂

        Reply
    12. J Clark

      November 25, 2016 at 4:16 am

      What is the nutritional value of each muffin?

      Reply
      • Marjory

        December 04, 2016 at 1:53 pm

        Hi! I'm so sorry but we don't currently offer nutritional information on the site.

        Reply
    13. Laura bourdeau

      October 03, 2017 at 12:40 pm

      If I want to make mini muffins - should I just half the recipe?

      Reply
      • Marjory

        October 04, 2017 at 10:41 am

        Hi! You can use the same recipe just use mini muffin tins and check after 20 minutes. They will cook faster. If you decide to half the recipe, still use 1 egg. I hope you enjoy them!

        Reply
    14. Jenna

      March 12, 2018 at 6:53 pm

      Can I use regular white flour or almond flour?

      Reply
      • Marjory

        March 12, 2018 at 8:04 pm

        Hi! Unbleached or bleached all purpose flour will definitely work. I've never tried almond flour and additional binding may be needed, such as adding another egg. If you try it, I'd love to know how it turns out!

        Reply
    15. Sarah

      May 21, 2018 at 6:20 pm

      1 star
      I had high hopes for these muffins but they did not work out. Even my pickiest eater wouldn't have more than a taste. Maybe my pumpkin was too watery? I didn't add the extra milk just in case. Disappointing.

      Reply
      • Marjory

        May 23, 2018 at 8:58 am

        I'm so sorry! What was the problem?

        Reply
    16. Paige

      October 01, 2018 at 12:20 pm

      5 stars
      I have made these twice now, and my family loves them! I used regular white whole wheat flour instead of whole wheat pastry flour, and regular plain yogurt instead of greek, because that is what I had on hand. I also reduced the sugar to 1/2 cup. Absolutely delicious, and I love that they are healthier than most muffin recipes. Thanks so much for the recipe, it is a keeper!

      Reply
      • Marjory

        October 01, 2018 at 5:37 pm

        Thanks so much for your tips and comment! I'm so glad you enjoyed them!

        Reply
    17. Pat

      October 17, 2018 at 4:05 pm

      I forgot the sugar. What should I do. The aren’t super sweet because of the chocolate chips

      Reply
      • Marjory

        October 18, 2018 at 7:14 am

        Hi! Here are some ideas for a topping: sprinkle powdered sugar on top, make a cream cheese frosting or make an easy orange drizzle by combining powdered sugar, and orange juice.

        Reply
    18. Katie

      October 15, 2019 at 7:26 pm

      5 stars
      Love that these are a healthier option than your typical muffins! They were still devoured like normal.

      Reply
      • Marjory Pilley

        October 16, 2019 at 6:57 am

        Thanks so much for your feedback!

        Reply
    19. Claudia

      October 15, 2019 at 8:16 pm

      5 stars
      Outstanding one look at that yummy muffin and I was drooling all over my keyboard..I am a huge pumpkin fan perfect...

      Reply
      • Marjory Pilley

        October 16, 2019 at 6:57 am

        I hope you enjoy them!

        Reply

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