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    Home » Recipes » Breads and Muffins

    Healthy Greek Yogurt Pumpkin Muffins

    UPDATED Oct 8, 2020 · PUBLISHED Oct 8, 2020 BY Marjory Pilley · This post may contain affiliate links. As an Amazon Associate I earn from qualifying purchases.

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    Stack of Healthy Greek Yogurt Pumpkin Muffins on a plate.

    These Greek yogurt pumpkin muffins are proof that healthy can also be delicious! Walkthrough the ingredient swaps that really make a difference!

    Two healthy Greek yogurt pumpkin muffins on a plate with one cut in half.

    I can't think of a better way to celebrate fall than with these healthy pumpkin muffins. Unless you're craving chocolate, in which case you may want to hop over to Healthy Chocolate Pumpkin Muffins!

    Either way, they always seem to be exactly what is needed. A quick breakfast? Afternoon snack? Lunch box treat? After dinner treat? Edible gift?

    I've yet to find an occasion when a delicious muffin doesn't do the trick! That's why you'll find so many variations using pumpkin, banana, and zucchini in our bread and muffin recipes section.

    As it turns out, you can enjoy pumpkin muffins, in limited quantities, even if you're counting carbs or calories! They're heavy on protein (from Greek yogurt, egg, and whole wheat flour) and fiber (from pumpkin and whole wheat flour) and can be low in sugar.

    I laid out all the ingredient choices below so you can customize this recipe and make the muffin of your dreams!

    Healthy Ingredient Swaps You Can Make

    My goal with this recipe was to give the traditional pumpkin muffin a healthy makeover without sacrificing taste. It was so successful that it became the recipe template for all our other muffins that use Greek yogurt.

    The graphic below shows the basic ingredients.

    Collage of the ingredients in the recipe for pumpkin muffins.

    You can "healthify" this recipe as little or as much as you would like. Here are the ingredient swaps we made:

    Whole Wheat Flour

    I generally use white whole wheat flour if I have it on hand. Otherwise, I use whole wheat flour.

    What's the difference? According to Bob's Red Mill, the difference between the two is the type of kernel that the flour is milled from. Whole wheat flour comes from a hard red berry and has a high protein content. On the other hand, white whole wheat comes from a hard white berry and has a moderate amount of protein.

    Another option is whole wheat pastry flour which comes from yet another type of berry: a soft white one. It has the lowest protein count of the three types but is also the most tender.

    All three retain the bran and germ which is what makes them a healthy option in my book.

    Oatmeal will work too. See how I adapted this recipe to make Healthy Oatmeal Pumpkin Muffins.

    Want to use almond flour? Check out low-carb baking with almond flour by All Day Long I Dream About Food if you want to go this route. You'll need to experiment to adapt this recipe.

    Greek Yogurt

    Replace canola or vegetable oil traditionally used in a pumpkin muffin recipe with Greek yogurt!

    This recipe uses a single-serve, 5.3-ounce container that you find in the grocery store. It measures out to be just a teaspoon or so short of ½ cup. Either measurement will work in this recipe.

    Sweetener

    I could take several pages to discuss the pros and cons of this ingredient. But, I'll keep it short. We used half the amount of sugar normally found in a traditional pumpkin muffin.

    Do they taste good with so little sugar? Yes, they absolutely do. I enjoy these all the time.

    It's very tasty if you're not used to super sugary baked goods. Mixing in something else sweet, such as dark chocolate or raisins also adds to the sweetness. I'll have more on those options in a minute.

    Can you use a powdered artificial sweetener like stevia, monk fruit, or erythritol? Yes! Use whatever sweetener you are used to baking with. But, don't drop below ½ cup of bulk or the muffins will be too soft. They will also have a slightly different texture and look.

    Can you use honey or maple syrup? Not in this recipe without making other ingredient adjustments. I love those sweeteners. But, I've never tried it in its recipe. If you want to go that route, A Whole New Mom has lots of good information on Baking with Honey and Maple Syrup.

    Can you use more sugar? Yes. This recipe will work with up to 1 cup of sugar.

    Mix-in Variations

    It's nice to have a little pop of sweetness with each bite of these pumpkin muffins since they're lower in sugar.

    • Dark Chocolate is my first choice. I am for 60-70% cacao. Semi-sweet chocolate chips are a type of dark chocolate and have a low sugar content too. Another option is stevia-sweetened morsels!
    • Raisins are a healthy choice but are higher in carbs than dark chocolate.
    • Nuts, such as walnuts, also work well in this recipe, especially if you combine them with chocolate!

    You can have a heavy hand when measuring out the mix-ins. I've never reached a limit, but I've never added more than ¾ of a cup either!

    Pumpkin Puree Tips

    I hope you can tell that these pumpkin muffins are not only healthy but also VERY moist. It's all because of the pumpkin puree. It does double duty as oil and egg.

    I'll let you in on a secret. You actually don't have to add Greek Yogurt or even egg to this recipe. Much like 2 Ingredient Pumpkin Muffins that uses a boxed cake mix, you'll end up with a muffin that is also vegan.

    Warning: Don't use pumpkin pie filling. It has sweetener and spices added to it. Buy a 15-ounce can that is pure pumpkin puree!

    Make-Ahead and Freezer Strategies

    Once pumpkin muffin season rolls around, I prepare batches of the dry mix in sealed containers or bags so it's a matter of minutes to have these baking in the oven and I never have to resort to less-healthy options to satisfy my cravings. This method gives you a little flexibility in case you decide to turn this into one of our other Greek yogurt muffins (there's a list below.)

    Another option is to cook and freeze them for up to 3 months. Store them in an air-tight bag or container. Or, individually wrap them in plastic wrap.

    When you're ready to enjoy one, microwave it for about 30 to 45 seconds on high or defrost overnight in the refrigerator.

    If I'm packing a snack for later, I just grab a frozen one and bring it along!

    Hand holding a healthy Greek yogurt pumpkin muffin with chocolate chips.

    Expert Baking Tips

    No matter which ingredient swaps you make, we've come up with a few key tips that will give you the best healthy pumpkin muffins every single time:

    • Spritz muffin tin wells OR paper inserts with cooking spray. There's no oil so this step is necessary. Although as the pumpkin muffins settle over the next few hours, it is not a problem.
    • Use mini-sized chips or roughly chop larger pieces of chocolate so that it more evenly distributes throughout the muffin.
    • Save a few chips to drop on top of each muffin just before baking. It's pretty!
    • Use an ice cream scoop to easily measure out a quarter cup of batter. The batter is thick and sticky.
    • Muffin topping idea: Healthy Cream Cheese Frosting made with Medjool dates instead of sugar!

    FAQ

    How many cups of pumpkin in a 15-ounce can?

    These are just under 2 cups of puree in a 15-ounce can. It's short 2 ½ Tablespoons.

    What can I substitute for pumpkin puree?

    Butternut squash, acorn squash, and sweet potato puree can all be used instead of pumpkin puree. We made this substitution to make Butternut Squash Muffins.

    How long do pumpkin muffins last?

    Store pumpkin muffins for 3-4 days in a sealed container. They don't need to be refrigerated. Store in the freezer for up to 3 months.

    Can you make these into mini muffins?

    Yes! Cook mini-sized muffins for about 15 minutes.

    Pumpkin Muffins stacked on a plate.

    More Greek Yogurt Muffin Recipes

    You'll find all our pumpkin muffin recipes in one place because the list is ever-growing! Other muffin recipes using yogurt you might want to check out:

    • Carrot Cake Muffins
    • Banana Muffins
    • Zucchini Muffins
    • Zucchini Blueberry Muffins
    • Chocolate Zucchini Muffins

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

    2 healthy Greek yogurt pumpkin muffins on plate with one cut in half.

    Healthy Greek Yogurt Pumpkin Muffins

    Greek yogurt pumpkin muffins are delicious and healthy from the easy ingredient swaps!
    4.5 from 4 votes
    Print Pin Rate
    Course: Breakfast, Snack
    Cuisine: American
    Prep Time: 10 minutes
    Cook Time: 25 minutes
    Total Time: 35 minutes
    Servings: 12 muffins
    Calories: 164kcal
    Author: Marjory Pilley

    Ingredients

    • 1 ½ cup white whole wheat flour any wheat flour will work
    • ½ cup sugar
    • ½ teaspoon baking powder
    • ½ teaspoon baking soda
    • ½ teaspoon salt
    • ½ teaspoon ground cinnamon
    • 15 ounce pumpkin puree 2 cups with 2 Tablespoons removed
    • 1 egg
    • 5.3 ounce Greek yogurt ½ cup
    • ½ cup Mini chocolate chips, semi-sweet or raisins

    Instructions

    • Preheat oven to 350 degrees F.
    • Combine flour, sugar, baking powder, baking soda, salt and cinnamon in a bowl.
    • Stir pumpkin, egg and yogurt into the dry mix.
    • Fold in mini chocolate chips.
    • Fill muffins tin wells coated with cooking spray about ⅔ full (about ¼ cup of batter.) Tip: if using liners, give them a light spritz of cooking spray too.
    • Bake for 20-25 minute or until the muffins are firm and lightly browned on the top.
    • Allow muffins to cool for 5 minutes in the pan and then remove to a wire rack to cool further. Enjoy!

    Notes

    There are more expert tips and helpful information in this post!
     
    Grab 5 Low-Carb Saucesand get more easy, healthy recipes! JOIN HERE

    Nutrition

    Calories: 164kcal | Carbohydrates: 27g | Protein: 5g | Fat: 5g | Saturated Fat: 2g | Cholesterol: 15mg | Sodium: 155mg | Potassium: 185mg | Fiber: 3g | Sugar: 14g | Vitamin A: 5540IU | Vitamin C: 1mg | Calcium: 48mg | Iron: 2mg
    Nutritional and Food Safety Disclaimer

    This recipe was originally published 9/16/2014. It was updated to improve the reader experience.

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    Reader Interactions

    Comments

    1. Taylor @ Food Faith Fitness

      September 17, 2014 at 8:08 am

      YAY for breaking out the pumpkin..I just did too!
      And these muffins? How much do you charge for shipping? 😉 Pinned!

      Reply
      • Marjory

        September 17, 2014 at 11:41 am

        Thanks Taylor! I love reading/trying all the new recipes that come out this time of year!

        Reply
    2. Nutmeg Nanny

      September 17, 2014 at 9:04 am

      These muffins look amazing! Love that they are so healthy with the whole wheat 🙂

      Reply
      • Marjory

        September 17, 2014 at 11:40 am

        Thanks! My girls love them...and don't even take notice that they've been made over.

        Reply
    3. claire @ the realistic nutritionist

      September 17, 2014 at 9:15 am

      Okay, these muffins look PERFECT.

      Reply
      • Marjory

        September 17, 2014 at 11:38 am

        Thanks so much!

        Reply
    4. christine

      September 17, 2014 at 9:25 am

      I love that these are a bit "healthified". Muffins can be deceiving in the healthy department sometimes. Great recipe and not as much guilt.

      Reply
      • Marjory

        September 17, 2014 at 11:38 am

        It's my "healthy" treat!

        Reply
    5. Laura O |Petite Allergy Treats

      September 17, 2014 at 9:28 am

      Love pumpkin and muffins! Let the pumpkin season begin!!

      Reply
      • Marjory

        September 17, 2014 at 11:37 am

        Thanks Laura! I'm ready!

        Reply
    6. Karli

      September 17, 2014 at 9:54 am

      Looks delicious!

      Reply
      • Marjory

        September 17, 2014 at 11:36 am

        Thanks! 🙂

        Reply
    7. Paula - bell'alimento

      September 17, 2014 at 10:25 am

      Pumpkin and Chocolate were made for each other.

      Reply
      • Marjory

        September 17, 2014 at 11:36 am

        I could not agree more!

        Reply
    8. Amanda @The Kitcheneer

      September 17, 2014 at 10:52 am

      I am loving these muffins! I too am about to plunge into all things pumpkin! And I am loving how much healthier these muffins are than traditional ones!

      Reply
      • Marjory

        September 17, 2014 at 11:36 am

        Thanks Amanda...can't wait to check out your pumpkin inspirations!

        Reply
    9. Crystal Barrett

      September 17, 2014 at 12:35 pm

      These look beautiful!!! I could eat a dozen of these right about now 🙂

      Reply
    10. Cate @ Chez CateyLou

      September 17, 2014 at 1:26 pm

      I can't get enough pumpkin lately! These muffins look amazing, and I love how healthy they are! What a perfect fall breakfast!

      Reply
    11. GiGi Eats

      September 17, 2014 at 2:22 pm

      Without pumpkin, I would NOT exist! LOL!

      Reply
    12. Rachel @ Bakerita

      September 17, 2014 at 2:49 pm

      There's few things I love more during the fall than pumpkin-anything with chocolate! These muffins look amazing, and I love that they're whole wheat too.

      Reply
    13. Ashley @ Wishes & Dishes

      September 17, 2014 at 3:27 pm

      Pass these my way! They look wonderful!

      Reply
    14. The Ninja Baker

      September 17, 2014 at 3:36 pm

      Only 100 calories, Marjory? Oh, my goodness they look soooo deliciously decadent...But how can I not make them keeping in my mind all the good for you ingredients =)

      Reply
    15. Alex @ DelishKnowledge

      September 17, 2014 at 5:46 pm

      Looks great! Yum! Love that you've made them healthier- I always laugh when I see muffin recipes that are similar in ingredients to cupcakes!

      Reply
    16. Kelli @Hungry Hobby

      September 17, 2014 at 6:32 pm

      Yum! I'm through two cans of pumpkin already and it's not even officially fall yet! It's going to be a pumpkin packed season for sure 🙂

      Reply
    17. Jeanette | Jeanette's Healthy Living

      September 17, 2014 at 7:38 pm

      Love this healthy pumpkin muffin - always looking for ways to reduce fat so I love the Greek yogurt!

      Reply
    18. Jenna

      September 17, 2014 at 7:53 pm

      How do you get pumpkin puree? May be a dumb question- but is it store bought in a can or do you roast a pumpkin in the oven or....?

      Reply
      • Marjory

        September 17, 2014 at 8:39 pm

        Hi! You can purchase 100% pure pumpkin in a can. 🙂

        Reply
    19. Angela {Mind Over Batter}

      September 18, 2014 at 9:58 pm

      Bring on the pumkin!!! These muffins look super duper moist and delicious. And it's a healthyfied muffin? Count me in!

      Reply
    20. kellie @ The Suburban Soapbox

      September 19, 2014 at 8:37 am

      These look amazing, they'll be making an appearance in lunch boxes next week!

      Reply
    21. Meseidy

      September 19, 2014 at 10:17 am

      I love pumpkin muffins!

      Reply
    22. Lauren @ Healthy Delicious

      September 21, 2014 at 10:29 am

      Pumpkin muffins are one of my favorites! I love that you made them whole wheat, too. Perfect for breakfast!

      Reply
    23. Mandy

      October 10, 2014 at 5:37 pm

      Have you tried substituting agave nectar for sugar in this recipe? Just wondering if it works?!
      Looks delicious- going to try these tonight! Maybe with a pumpkin beer 😉

      Reply
      • Marjory

        October 10, 2014 at 6:42 pm

        I haven't tried it...but, it sounds like a good idea! I hope you enjoy it!

        Reply
    24. Beekers

      October 12, 2014 at 6:38 pm

      I made these today. They are really good. I used Truvia baking blend instead of sugar and I added some pumpkin pie spice. My husband said I could make them again!

      Reply
      • Marjory

        October 12, 2014 at 7:44 pm

        Awesome! Thanks for sharing. I like it with a blend too...I've got one that's part sugar and part stevia.

        Reply
    25. Hayley L

      October 25, 2014 at 9:21 pm

      Hello! Do you have the nutrition facts for these? I need to know the carb count for the diabetics in my family
      I made them and my family loved them! Great texture and taste
      Thanks!

      Reply
      • Marjory

        October 26, 2014 at 8:00 am

        Thanks for your comment. Unfortunately, we do not have nutrition software at this time. 🙁 I sometimes use an app like My Fitness Pal to get some estimates though, like the calorie count that I provided.

        Reply
    26. Lisa

      November 16, 2014 at 6:59 pm

      Hi these muffins came it delish! Only problem is they didn't really rise up. Any reason why? Thanks!

      Reply
      • Marjory

        November 17, 2014 at 11:34 am

        Thanks for your comment. I'm really not sure why they didn't rise because I make these at least once a week with no troubles. I had this happen on another recipe I make frequently (vegan chocolate cake) and I think my baking powder was stale...just a thought!

        Reply
    27. pamela

      January 25, 2015 at 4:59 pm

      5 stars
      Just made these. Hot out of the oven and delish. Good thing I doubled the recipe as my 10 year old son loves them. Calculated 3 weight watchers points per muffin. Yum.

      Reply
    28. Kristina

      November 02, 2015 at 4:17 pm

      5 stars
      I've made these twice now and learned my lesson--double the recipe. They go fast. My family loves them! Today I used stevia sweetened chocolate and topped each muffin with a pecan. Great recipe; thank you!

      Reply
      • Marjory

        November 03, 2015 at 8:27 pm

        Thanks for sharing your experience with stevia sweetened chocolate! Yum!

        Reply
    29. Em

      November 08, 2015 at 8:13 pm

      3 stars
      I loved finding a recipe that uses whole wheat and real pumpkin in place of oils. However, I would advise doubling the spices, it lacked a pop of flavor I love with Fall pumpkin dishes.

      Reply
      • Marjory

        November 13, 2015 at 11:49 am

        Thanks for your tip!

        Reply
    30. Sara

      May 17, 2016 at 12:35 am

      Do you use plain or vanilla Greek yogurt?

      Reply
      • Marjory

        May 17, 2016 at 8:25 am

        Hi! I've only used plain Greek yogurt, but I bet vanilla would be delicious!

        Reply
    31. Sara

      May 27, 2016 at 12:50 am

      I know it's not fall and pumpkin season, but I've had a can of pumpkin staring at me each time I open my pantry, so I just really wanted to make these. ???? I'm not a huge baker, so I can't figure out what I did wrong. My muffins rose in the oven and then fell immediately and were very dense and heavy and kinda mushy in the middle. They were not pretty and fluffy like yours. Any ideas as to what I may have done wrong?

      Reply
    32. Brittany

      October 14, 2016 at 11:38 pm

      These are awesome! I added some pumpkin pie spice and used kefir and a little oil since I didn't have Greek yogurt and they turned out fantastic! Thanks!!

      Reply
      • Marjory

        October 15, 2016 at 11:17 am

        Sounds yummy! Thanks for sharing!

        Reply
    33. Althan

      November 09, 2020 at 8:31 am

      5 stars
      Good recipe. Healthy. I added unsweetened applesauce, about half a cup. I substituted low-fat plain yogurt because I didn’t have a Greek one. The muffins did have to bake 45 minutes because of applesauce I think. I got 14 muffins. I did spritz the cupcake liners on the bottom with the Pam spray. But the muffins did stick to the paper liners which has happened to me before with recipes that don’t have any oil or butter or some type of fat in the content. Next time, I will not add the applesauce and I will probably add about a 1/4 cup of vegetable oil. I think it still will be healthy and will alleviate the stickiness issue. Thank you for a delicious recipe.

      Reply
      • Marjory Pilley

        November 09, 2020 at 8:59 am

        Thanks for your tips for the applesauce and I'm so glad you enjoyed then! Did you use that in place of sugar?

        Reply

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