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







Kristina says
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 says
Thanks for sharing your experience with stevia sweetened chocolate! Yum!
pamela says
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 says
Hi these muffins came it delish! Only problem is they didn't really rise up. Any reason why? Thanks!
Marjory says
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 says
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 says
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 says
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 says
Awesome! Thanks for sharing. I like it with a blend too...I've got one that's part sugar and part stevia.
Mandy says
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 says
I haven't tried it...but, it sounds like a good idea! I hope you enjoy it!
Lauren @ Healthy Delicious says
Pumpkin muffins are one of my favorites! I love that you made them whole wheat, too. Perfect for breakfast!