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These Greek yogurt pumpkin muffins are proof that healthy can also be delicious! Walk through the ingredient swaps that really make a difference!
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!
Jump to:
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.
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!
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
These are just under 2 cups of puree in a 15-ounce can. It's short 2 ½ Tablespoons.
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.
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.
Yes! Cook mini-sized muffins for about 15 minutes.
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:
Would you like more easy, healthy, carb-conscious recipes?
📋 Recipe
Healthy Greek Yogurt Pumpkin Muffins
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 or pumpkin spice blend
- 1 ½ cups pumpkin puree 15-ounce can with 2 Tablespoons removed
- 1 egg
- ½ cup Greek yogurt 5.3 ounce container
- 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 about 25 minutes 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
Nutrition
This recipe was originally published 9/16/2014. It was updated to improve the reader experience.
Jessica
I made these last night to have something cozy for our snow storm. They are EXCELLENT! My new go-to.
Marjory Pilley
I’m so happy you enjoyed them!
Sarah
Yum! I made these to use up leftover pumpkin puree and they were delicious and easy to make. I actually had leftover cinnamon sugar from a previous recipe, so I rolled them in melted butter and dipped them in cinnamon sugar. (and so skipped the chocolate chips)
Sandy
Just made them! And ate two!! Wonderful recipe. I used coconut sugar instead of regular sugar. Love these lightly sweetened, healthy pumpkin muffins.
Pat
These are delicious! I used date sugar for added fiber and the entire can of pumpkin and they came out great. I omitted the add-ins but will definitely make again adding walnuts next time.
It's a keeper!
Marjory Pilley
I'm so happy you enjoyed them! Thanks for sharing your experience.
JoJo
Wonderful recipe but it is very dense.
Suzi
Love that the recipe calls for a whole can of pumpkin(the extras always sit in my freezer too long.) I found these tasty but a little too moist. I will try the add ins you suggested next time to add more texture. Thank you!
Alandra
Really yummy!! I used almond flour, and if you want to use almond flour too, I recommend adding another egg, using silicone cupcake liners, and baking at 375° for 30 minutes!!
Marjory Pilley
Thanks so much for your tips on using almond flour!
Carole
thanks for the tip using Almond flour
Althan
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.
Marjory Pilley
Thanks for your tips for the applesauce and I'm so glad you enjoyed then! Did you use that in place of sugar?
Brittany
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!!
Marjory
Sounds yummy! Thanks for sharing!
Sara
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?
Janet
Sounds like you didn't bake them fully. Before removing from the oven stick a toothpick into one in the center of the tray and see if it comes out dry or with a few crumbs. If there is still uncooked batter then they need more time. I usually do 3-5 more minutes and check again.
Sara
Do you use plain or vanilla Greek yogurt?
Marjory
Hi! I've only used plain Greek yogurt, but I bet vanilla would be delicious!
Em
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.
Marjory
Thanks for your tip!
Kristina
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!
Marjory
Thanks for sharing your experience with stevia sweetened chocolate! Yum!
pamela
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.
Lisa
Hi these muffins came it delish! Only problem is they didn't really rise up. Any reason why? Thanks!
Marjory
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!
Hayley L
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!
Marjory
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.
Beekers
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!
Marjory
Awesome! Thanks for sharing. I like it with a blend too...I've got one that's part sugar and part stevia.
Mandy
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 😉
Marjory
I haven't tried it...but, it sounds like a good idea! I hope you enjoy it!
Lauren @ Healthy Delicious
Pumpkin muffins are one of my favorites! I love that you made them whole wheat, too. Perfect for breakfast!
Meseidy
I love pumpkin muffins!
kellie @ The Suburban Soapbox
These look amazing, they'll be making an appearance in lunch boxes next week!
Angela {Mind Over Batter}
Bring on the pumkin!!! These muffins look super duper moist and delicious. And it's a healthyfied muffin? Count me in!
Jenna
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....?
Marjory
Hi! You can purchase 100% pure pumpkin in a can. 🙂
Jeanette | Jeanette's Healthy Living
Love this healthy pumpkin muffin - always looking for ways to reduce fat so I love the Greek yogurt!
Kelli @Hungry Hobby
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 🙂
Alex @ DelishKnowledge
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!
The Ninja Baker
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 =)
Ashley @ Wishes & Dishes
Pass these my way! They look wonderful!
Rachel @ Bakerita
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.
GiGi Eats
Without pumpkin, I would NOT exist! LOL!
Cate @ Chez CateyLou
I can't get enough pumpkin lately! These muffins look amazing, and I love how healthy they are! What a perfect fall breakfast!
Crystal Barrett
These look beautiful!!! I could eat a dozen of these right about now 🙂
Amanda @The Kitcheneer
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!
Marjory
Thanks Amanda...can't wait to check out your pumpkin inspirations!
Paula - bell'alimento
Pumpkin and Chocolate were made for each other.
Marjory
I could not agree more!
Karli
Looks delicious!
Marjory
Thanks! 🙂
Laura O |Petite Allergy Treats
Love pumpkin and muffins! Let the pumpkin season begin!!
Marjory
Thanks Laura! I'm ready!
christine
I love that these are a bit "healthified". Muffins can be deceiving in the healthy department sometimes. Great recipe and not as much guilt.
Marjory
It's my "healthy" treat!
claire @ the realistic nutritionist
Okay, these muffins look PERFECT.
Marjory
Thanks so much!
Nutmeg Nanny
These muffins look amazing! Love that they are so healthy with the whole wheat 🙂
Marjory
Thanks! My girls love them...and don't even take notice that they've been made over.
Taylor @ Food Faith Fitness
YAY for breaking out the pumpkin..I just did too!
And these muffins? How much do you charge for shipping? 😉 Pinned!
Marjory
Thanks Taylor! I love reading/trying all the new recipes that come out this time of year!