These Greek yogurt pumpkin muffins are lightly sweetened and made with whole wheat flour. Pumpkin puree and Greek yogurt make them incredibly moist, while chocolate chips add little bursts of sweetness in every bite. They're a healthy fall snack that is simply irresistible.


Notes from my kitchen
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!
My goal with this recipe was to give the traditional pumpkin muffin a makeover without sacrificing taste. It was so successful that it became the template for most of our other muffins!
Greek yogurt replaces the oil and, along with plenty of pumpkin puree, makes these muffins extremely tender. Whole wheat flour adds extra fiber and a little protein, and I cut back on the sugar, too.
Below I've included all the ingredient options I've tested so you can customize these Greek yogurt pumpkin muffins just the way you like.
Marjory
Jump to:
Ingredients
Here's what I used to make these Greek yogurt pumpkin muffins:

Of special note:
- Whole wheat flour - White whole wheat flour is my usual choice because it is easier to find, but whole wheat pastry flour makes an especially soft, tender muffin. Both are whole-grain flours, but pastry flour is made from softer wheat and has less protein, so it develops less gluten. If you're using regular whole wheat flour, I recommend a 50/50 mixture of whole wheat and all-purpose flour for a lighter texture. For an oat-based version, see my healthy oatmeal pumpkin muffins.
- Greek yogurt replaces the canola or vegetable oil traditionally used in pumpkin muffins and, with the pumpkin puree, keeps them moist and tender. You'll need ½ cup. A 5.3-ounce single-serve container is just a teaspoon or so shy of that amount and works perfectly, too. I use plain nonfat Greek yogurt so it doesn't compete with the pumpkin and spices.
- Pumpkin puree - Use a 15-ounce can of pure pumpkin puree, not pumpkin pie filling, which already contains sweeteners and spices. Simply remove 2 tablespoons from the can and use the rest in the muffins. All that pumpkin keeps them very moist. And don't toss the leftover pumpkin. It's just enough to make my pumpkin chaffles.
- Sugar and sugar alternative: I use ½ cup total of sweetener, which is about half what you'll find in many traditional pumpkin muffin recipes. I use a blend of regular sugar and a granulated sugar alternative to reduce the added sugar even more. Use a sugar alternative you're comfortable baking with and follow the manufacturer's substitution recommendations. I don't recommend reducing the total amount below ½ cup because the sweetener also contributes to the muffins' texture and structure. You can use all regular sugar and increase it up to 1 cup if you prefer an even sweeter muffin.
- Chocolate chips add little bursts of sweetness in every bite. I like mini chocolate chips because they distribute more evenly throughout the batter. I look for the darkest chocolate I can find. Semi-sweet, chopped dark chocolate and stevia-sweetened chips work great. Raisins or chopped walnuts are nice variations, or use a combination. 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!
The recipe card below includes ingredient amounts, step-by-step instructions, and nutritional information.
How to make Greek yogurt pumpkin muffins
Use these pictures as a guide in making the recipe. The complete instructions are in the recipe card.
Mix the batter

Mix the dry ingredients, add the wet ingredients, and stir just until combined, then gently fold in the chocolate chips.
Fill the muffin pan

Fill greased muffin tin wells about ⅔ full. A cookie or ice cream scoop makes portioning the batter easy. If you're using paper liners, lightly spritz them with cooking spray too to prevent sticking.
Bake

Bake until the tops are firm and lightly browned. Cool in the pan for 5 minutes, then transfer the muffins to a wire rack to finish cooling.
Make-Ahead and Storage
Store cooked muffins in an airtight container on the counter for 2 days and up to 5 days in the refrigerator.
Once pumpkin muffin season rolls around, I prepare batches of the dry mix in sealed containers or bags so it takes minutes to have these baking in the oven. This method also gives you a little flexibility if you decide to turn this into one of our other Greek yogurt muffins.
Another option is to cook and freeze them for up to 3 months. Store them in an airtight bag or container. Or wrap them individually 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 to defrost during the day!

FAQ
Yes! Cook mini-sized muffins for about 15 minutes.
Yes. Plain Greek yogurt works best, and you can use nonfat, 2%, or whole-milk Greek yogurt. Higher-fat yogurt may make the muffins slightly richer. I recommend avoiding flavored or sweetened yogurt because it can change the muffins' sweetness and flavor. Regular yogurt is thinner than Greek yogurt, so I don't recommend this substitution.
Not in this recipe without making other ingredient adjustments. I love those sweeteners. But I've never tried it in this recipe.
More Greek Yogurt Muffin Recipes
Other muffin recipes using Greek yogurt you might want to check out:
Would you like more easy, healthy, carb-conscious recipes?
📋 Recipe

Healthy Greek Yogurt Pumpkin Muffins
As an Amazon Associate, I earn from qualifying purchases.
Ingredients
- 1 ½ cup white whole wheat flour whole wheat pastry flour or a mixture of ½ whole wheat flour and ½ all-purpose flour
- ½ cup Sugar blend (half real sugar) or ½ cup granulated sugar. See notes on more options
- ½ teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon salt
- ½ teaspoon pumpkin spice blend or ground cinnamon
- 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, walnuts
Instructions
- Preheat oven to 350℉.
- Combine flour, sugar, baking powder, baking soda, salt and pumpkin pie spice (or cinnamon) in a large bowl.
- Stir pumpkin, egg and yogurt into the dry mix, just until combined.
- Fold in mini chocolate chips.
- Fill muffin tin wells coated with cooking spray about ⅔ full (about ¼ cup of batter). 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 transfer to a wire rack to cool further.
Notes
Use at least ½ cup total sweetener for the best texture and structure. I use a blend of sugar and a granulated sugar alternative to reduce added sugar. All regular sugar works, too, and you can increase the total to 1 cup for even sweeter muffins.
Want to save this recipe?
I'll also send you other recipes I know you'll love. Unsubscribe at any time.
Nutrition
This recipe was originally published 9/16/2014. It was updated to improve the reader experience.







Paula - bell'alimento says
Pumpkin and Chocolate were made for each other.
Marjory says
I could not agree more!
Karli says
Looks delicious!
Marjory says
Thanks! 🙂
Laura O |Petite Allergy Treats says
Love pumpkin and muffins! Let the pumpkin season begin!!
Marjory says
Thanks Laura! I'm ready!
christine says
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 says
It's my "healthy" treat!
claire @ the realistic nutritionist says
Okay, these muffins look PERFECT.
Marjory says
Thanks so much!
Brandi says
can I use coconut flour? I'm allergic to other flours and almond flour as well.
Marjory Pilley says
Coconut flour does not substitute one for one with whole wheat or all purpose flour. It absorbs liquids very easily and generally would need only 1/4 to 1/3 cup of coconut flour for every cup of whole wheat. I’ve not made the muffins with this substitution and other changes to the ingredients and instructions would need to be made as well!
Nutmeg Nanny says
These muffins look amazing! Love that they are so healthy with the whole wheat 🙂
Marjory says
Thanks! My girls love them...and don't even take notice that they've been made over.
Taylor @ Food Faith Fitness says
YAY for breaking out the pumpkin..I just did too!
And these muffins? How much do you charge for shipping? 😉 Pinned!
Marjory says
Thanks Taylor! I love reading/trying all the new recipes that come out this time of year!