Healthy Greek Yogurt Pumpkin Muffins

by Beat Bake Eat

This easy recipe for homemade Healthy Pumpkin Muffins is quick, simple, and the best. They’re naturally sweetened, low calorie, low fat, and kid-friendly. The perfect healthy Fall breakfast recipe for using up pumpkin puree.

Healthy Greek Yogurt Pumpkin Muffins - Soft, moist whole wheat pumpkin muffins made with pumpkin puree. Perfect for a Fall breakfast.

It’s October everyone! Wow, time really flies. I swear school just started and now it’s been a whole month. Now that fall season is here it’s time for all things spooky and all things pumpkin.

I hate the cold weather but I do love watching the leaves change and watching them turn into beautiful colors and falling off the trees, and I also love having healthy pumpkin muffins for breakfast.

I remember, many years ago, I used to think that making pumpkin muffins from scratch was so hard. The only types of muffins that I used to make were banana muffins. In fact, I used to be so skeptical about baking with canned pumpkin puree. I really was! I grew up in the Caribbean so baking with pumpkin seemed very odd to me. But the minute I tried it, I was hooked!

I’ve also come to love baking with Greek yogurt. I used to be so skeptical about that too. But baked goods with Greek yogurt always turn out so soft. These low fat, pumpkin Greek yogurt muffins are definitely one of my favorite breakfast recipes to date.

And with all the (sugary, fattening) baking that happens in Fall and around Thanksgiving, this healthy pumpkin recipe is one you won’t feel guilty about.

This recipe has all of the great flavors you love when it comes to pumpkin muffins but without all of the extra calories. These low calorie pumpkin muffins are made with one whole cup of canned pumpkin puree. Oh, yes. We’re not skimping on the pumpkin flavor today my friends. They’re also made with vegetable oil and Greek yogurt which makes them so soft and moist, and they have no sugar in them.

Healthy Greek Yogurt Pumpkin Muffins - Soft, moist whole wheat pumpkin muffins made with pumpkin puree. Perfect for a Fall breakfast.

Healthy Pumpkin Muffin Ingredients

The ingredient list for these muffins is short and simple. Here’s what you’ll need:

  • Pumpkin puree – you can’t make these muffins without pumpkin puree so grab a can or make your own.
  • Maple syrup or honey – perfect all-natural sweeteners that are much better for you than refined sugar.
  • Greek yogurt and vegetable oil – for softness and moisture.
  • Vanilla extract and salt– for added flavor and to enhance flavor.
  • Whole wheat flour – for fiber, health, and lower cholesterol. Woo!
  • Cinnamon and nutmeg – spice and all things nice.
  • Baking soda, baking powder, and one egg– for leavening, structure, and texture.

These muffins are pumpkin puree muffins. They’re not made with filling so make sure that your can of pumpkin puree says ‘100% pumpkin’. You don’t want to end up using pie filling in this recipe because it’s much sweeter and that would defeat the whole point of these muffins being healthy.

Because these healthy pumpkin muffins with yogurt are made completely without sugar I had to substitute with maple syrup or honey. Feel free to use whichever one you want. It doesn’t really matter. They’re just used for sweetness, not flavor. I used maple syrup because I absolutely love it and I love anything maple-flavored (even though the pumpkin kind of overpowered it in these muffins). And I made sure to put 2 teaspoons of vanilla extract in this recipe to really amp up the flavor.

Maple syrup is so expensive though. Damn… but it’s definitely worth every drop!

For those of you who aren’t accustomed to baking with Greek yogurt you might be wondering why use Greek yogurt and not just regular yogurt? Well, Greek yogurt has less lactose which means that it contains less sugar than regular yogurt. And while it is much denser, it’s lower in carbs, lower in fat and high in protein. It also has a slightly tangy flavor to it which pairs well with sweet baked goods. I chose to use 2% Greek yogurt in this recipe because it’s full fat and is therefore richer in flavor. I don’t recommend using nonfat Greek yogurt because it would most likely change the taste and the texture of the muffins. You can use either plain or vanilla yogurt for this recipe.

Quick tip: If you don’t have Greek yogurt on hand you can also use sour cream. I know that it’s higher in calories and not as healthy as Greek yogurt however, it’s a great last resort alternative.

And because of the Greek yogurt and the oil there is no butter and no milk in this recipe. Oh, and these healthy pumpkin muffins have no oats. I thought of adding them for a split second but I decided not to and I’m very happy with my decision.

Healthy Greek Yogurt Pumpkin Muffins - Soft, moist whole wheat pumpkin muffins made with pumpkin puree. Perfect for a Fall breakfast.

How to make Healthy Pumpkin Muffins

Even though this is a two-bowl recipe it’s still quick and easy to make.

{Full recipe below}

  1. Preheat your oven to 350°F. Prep the muffin pan and set aside.
  2. Combine the pumpkin puree, maple syrup/honey, and greek yogurt in a large bowl.
  3. Beat in the oil, egg, and vanilla extract.
  4. Whisk together the dry ingredients (the remaining ingredients), add them to the wet ingredients and stir until incorporated.
  5. Evenly distribute the batter between the 12 muffin cups and bake.
  6. Cool and enjoy!

See? Simple steps. Making healthy pumpkin muffins is quite easy so prepare yourself for the aroma that is going to fill your kitchen. You’re going to love it!

The batter for this recipe is quite thick because there’s not much liquid but it makes it very easy to scoop into the muffin cups without making a huge mess. I’m guilty of this sometimes.

I must say that these muffins baked up perfectly. I baked mine for 20 minutes but I suggest that you check them at the 18-minute mark just to be safe.

When these homemade muffins come out of the oven they’re not going to be the prettiest things you’ve ever seen, but they sure will be one of the most delicious! They have big bumps and they look like if they were to be thrown, they could cause some damage, but they’re actually really soft. You’ll see what I’m talking about.

These muffins are so good fresh from the oven though. I mean, all muffins are great fresh from the oven but these are amazing. You can say that these orange-tainted beauties are like little pumpkin pie muffins.

If you’re not able to have them right away or if you’re having them for breakfast the next day, feel free to reheat them in the microwave. That’s exactly what I did.

If you’d like to use pumpkin spice in place of the cinnamon and nutmeg go right ahead. I’m sure it would make these muffins even more delicious.

Also, I only used one egg in this recipe because I’ve noticed that pumpkin recipes don’t need much aeration. In fact, you can even replace eggs with pumpkin puree. They’re actually used as an egg substitute in recipes all the time. I didn’t even know this until recently.

Freezing and storage:

  • Can pumpkin muffins be frozen? Yes, they can. They can be frozen and then thawed at room temperature or you can heat them in the microwave for about 20 seconds or so (it will depend on your specific microwave). You can also reheat them in the oven by wrapping them in foil and baking them at 350°F for 10 – 15 minutes or until they are completely warmed through.
  • You can store these pumpkin muffins in an airtight container or zippy bag. They should keep for two days.

Healthy Greek Yogurt Pumpkin Muffins - Soft, moist whole wheat pumpkin muffins made with pumpkin puree. Perfect for a Fall breakfast.

Kid-Friendly Pumpkin Muffins

Although it seems far away, Halloween is actually right around the corner and so these muffins are great for a healthy pumpkin snack that you don’t have to feel guilty about or have to feel bad about giving to the kids, especially after they have all of that candy. They’re great for the Lunchbox since they’re sugar free and high in fiber.

I’ve said this before but, I love healthy muffins. I think I love them more than white flour muffins because muffins made with whole wheat flour are so much more filling. And I know if you’re new to the world of baking with whole wheat flour they can seem like they have a harsh texture but they don’t if you put the right ingredients in your recipe. They can actually be really delicious and much tastier than regular muffins. And these muffins are so fluffy and scrumptious that your kids, or your toddler, will not care that they’re made with whole wheat flour. They are that magical. They can convert anyone.

This is going to be your new favorite healthy pumpkin muffin recipe because it’s so easy to make and really delicious too. You definitely need to add this one to your list of easy pumpkin recipes because it is packed with Fall flavor despite it being a healthier breakfast option. It’s just perfect and that’s why it’s the best. If you’re looking for a healthy, low calorie, canned pumpkin recipe, this is a great one!

There’s a few more whole wheat flour muffin recipes here on Beat Bake Eat. You should check them out! You gotta love easy baking recipes.

Healthy Greek Yogurt Pumpkin Muffins - Soft, moist whole wheat pumpkin muffins made with pumpkin puree. Perfect for a Fall breakfast.

As soon as Fall hits I always like to keep a can of pumpkin puree in the house because there’s lots of canned pumpkin recipes to be made, especially the baking kind.

I’m currently brainstorming new pumpkin puree breakfast recipe ideas, so if you think of any good ones please let me know in the comments below!

I might end up doing more recipes of this kind because I love homemade healthy muffins, especially when they’re low fat and sugar free. They always make for a guilt-free breakfast.

It seems that when I get started with the healthy pumpkin breakfast recipes, I don’t stop.

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Healthy Greek Yogurt Pumpkin Muffins - Soft, moist whole wheat pumpkin muffins made with pumpkin puree and perfect for a Fall breakfast.

Healthy Greek Yogurt Pumpkin Muffins

Beat Bake Eat
This easy recipe for homemade Healthy Pumpkin Muffins is quick, simple, and the best. They’re naturally sweetened, low calorie, low fat, and kid-friendly. The perfect Fall breakfast recipe for using up pumpkin puree.
4.59 from 34 votes

Click the stars to rate!

Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Course Breakfast, Snack
Cuisine American
Servings 12 muffins
Calories 184 kcal


  • 1 cup canned pumpkin puree
  • 2/3 cup maple syrup or honey
  • 1/4 cup 2% Greek yogurt, plain or vanilla
  • 1/4 cup vegetable oil
  • 1 egg
  • 2 teaspoons vanilla extract
  • 1 2/3 cups whole wheat flour
  • 1 teaspoon cinnamon
  • 1/4 teaspoon nutmeg
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon baking powder
  • 1/2 teaspoon salt


  • Preheat oven to 350°F. Line muffin pan with muffin liners and set aside.
  • In a large bowl combine the pumpkin puree, maple syrup/honey, and Greek yogurt.
  • Beat in the oil, egg, and vanilla extract.
  • In another large bowl whisk together the flour, cinnamon, nutmeg, baking soda, baking powder, and salt. 
  • Add the dry ingredients to the wet ingredients and stir until incorporated (batter will be thick). Do not over mix.
  • Scoop the batter into the muffin pan distributing it evenly between the muffin cups.
  • Bake for 18 - 20 minutes.
  • Cool in pan 10 minutes then remove.


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Keyword healthy pumpkin recipes, how to make healthy pumpkin muffins, pumpkin puree muffins
Tried this recipe?Let me know how it was!
Healthy Greek Yogurt Pumpkin Muffins - Soft, moist whole wheat pumpkin muffins made with pumpkin puree and perfect for a Fall breakfast.
Healthy Greek Yogurt Pumpkin Muffins - Soft, moist whole wheat pumpkin muffins made with pumpkin puree and perfect for a Fall breakfast.
Healthy Greek Yogurt Pumpkin Muffins - Soft, moist whole wheat pumpkin muffins made with pumpkin puree and perfect for a Fall breakfast.

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Recipe Rating


Laura August 26, 2019 - 2:23 pm

I made these today. I used maple syrup for the sweetener and non-fat high protein Greek yogurt. I also added a 1/8 – 1/4 tsp ground ginger to the spices the recipe called for. These are delicious and added to my favorites.

Crystal August 26, 2019 - 8:05 pm

That sounds delicious! I’m gonna add some ground ginger the next time I make these. Thanks for leaving a comment, Laura!

Angie September 24, 2019 - 12:47 am

Could you substitute coconut oil for the vegetable oil?

Crystal September 24, 2019 - 4:56 pm

Yes, as long as it is melted, not solid.

Marie F October 11, 2019 - 1:35 am

These were so moist and fluffy! I used maple syrup and they had the perfect amount of sweetness. I added ginger as well, along with some allspice and cardamom, just because Im a spice addict!! Made them last week, and currently have another batch in the oven! Thank you!

Crystal October 11, 2019 - 11:30 am

Thank you so much for the 5-star review, Marie! I’m sure those additional spices made the muffins even more delicious.

Marie October 11, 2019 - 1:40 am

Ive now made 2 batches of these delicious healthy muffins. I used maple syrup and it was the perfect sweetness. I also added ginger, along with 1/4 tsp allspice and cardamom, but Im a spice freak!! Thank you for a great autumn muffin!

Crystal October 11, 2019 - 11:32 am

You’re very welcome! ? I appreciate your feedback.

Susan October 13, 2019 - 4:05 pm

What size canned pumpkin?

Susan October 13, 2019 - 4:06 pm

Ooops never mind….

Crystal October 13, 2019 - 4:23 pm


Mo C October 20, 2019 - 2:46 pm

Just made these!! The maple syrup was a nice touch (I had to add a little honey to make the amount work). Smelled great baking. Delicious! First time using whole wheat flour, couldn’t tell difference!! Added this to the recipe box!!!

Crystal October 20, 2019 - 5:37 pm

Yay! This is what I aim for! I always make sure that my whole wheat baked goods don’t have that “whole wheat taste”. I’m so glad you like them, Mo. Maple and pumpkin is a fabulous combo. Thank you for stopping by and leaving a comment!

Maureen October 20, 2019 - 6:30 pm

This looks delicious! How many points each?

Crystal October 20, 2019 - 9:18 pm

Thank you, Maureen! I’m assuming you mean weight watchers points? To be honest I don’t know much about that program but I used a smart points calculator that I found online and the answer I got is 7 points. I hope this helps!

Kim R. November 11, 2019 - 3:56 pm

I quickly found this recipe while standing in front of the canned pumpkin in the grocery store. When I got home and gathered my ingredients to bake, I realized I was out of nutmeg! I searched through comments and decided to use 1/4 tsp each of ground ginger and cardamom instead. Then I realized I only had about 1/3 C of honey. I added some semisweet chocolate chips to try to make up for the lack of sweetener. I was so nervous that I’d ruin the recipe! To my surprise, the muffins turned out perfectly! They were just sweet enough, and had the perfect amount of spice. They will make the perfect breakfast muffins 🙂 I’m totally saving this recipe!

Crystal November 11, 2019 - 6:15 pm

Wow. That’s some quick thinking! Pretty much any kind of Autumn spice will work in this recipe. Adding the chocolate chips was a great idea! I’m so glad it all worked out. Thanks for the review, Kim!

Josnne November 24, 2019 - 6:33 pm

I. Making the muffins now. Have been in the oven for 20 minutes. Muffin s don’t look done but I’m anxious to try them,

Crystal November 24, 2019 - 11:40 pm

How long did you end up baking them for? I hope you enjoyed!

Theresa McMahon November 24, 2019 - 9:39 pm

Would this work, using gluten free flour?

Crystal November 24, 2019 - 11:38 pm

I’m not sure because I’ve never tried it myself but I did a little research and I think it could work. People do it all the time with muffin recipes. If you do give it a try let me know how it turns out!

Canadian Carol December 19, 2019 - 11:37 am

Thanks for posting the recipe. I added 1/4 tsp each of ginger and allspice. I used 1/2 C of maple syrup to reduce the sugar, but might try 2/3 C next time. I am wondering why the quantity of baking soda and baking powder is not 1 tsp each. Also, the muffin recipes I find online usually have 1.5 cups of flour. Do you prefer that added 1/6 C of flour? The muffins are moist and delicious. I like adding 2% greek yogurt to all the muffins I make too.

Crystal December 19, 2019 - 1:11 pm

You’re very welcome, Canadian Carol! (Awesome name, by the way)
I find that the amount of honey/maple syrup in this recipe is perfect. Any less and the muffins taste a little under sweetened.
I believe that in this case 1 teaspoon each of baking soda and baking powder would be too much because the only ingredient in this recipe that is acidic enough to neutralize the baking soda is the honey/maple syrup. In any recipe, if the baking soda is not neutralized, the baked good ends up with a metallic taste which you definitely do not want!
The amount of flour in this recipe is not about preference but about how much is needed to hold and bind all of the wet ingredients together to provide the perfect structure and texture.
I’m so happy that you like the muffins and thank you for taking the time to leave a comment to let me know! ?

Ashley October 11, 2020 - 8:22 am

I don’t have any whole wheat flour on hand can I use white flour?

Crystal | Beat Bake Eat October 11, 2020 - 9:55 am

I think you can but the texture would be different and they may need to be baked a little longer since all-purpose flour doesn’t soak up as much moisture as whole wheat.

GJ Hiscock November 1, 2020 - 11:49 am

To make these great muffins even healthier, substitute applesauce for vegetable oil.
Since I had more than 1 cup of pumpkin I reduced the maple syrup.
Crushed walnuts/pecans will be added the next time.

Crystal | Beat Bake Eat November 2, 2020 - 6:32 pm

I’m glad those substitutions worked out for you! I think the pecans would be a really nice addition. Thanks for leaving a comment!

Sandra November 29, 2020 - 9:18 am

I made the muffins with oatmeal flour. I used unsweetened applesauce instead of oil. I also used Walden Farms pancake syrup for a 0 calorie substitution for the maple syrup. I had to increase the baking time by 15 minutes, probably because of my substitutions, but the very low calorie reward was worth it. Thanks for your recipe.

Crystal | Beat Bake Eat November 29, 2020 - 1:33 pm

I’m happy those substitutions worked out for you, Sandra! Thank you so much for leaving a comment.

Rebecca September 26, 2021 - 11:48 am

I tried it today: normal yogurt instead of Greek yogurt and wholemeal flour, a sprinkle of brown sugar on top. It turned out great, extremely soft, perfect really!

Beat Bake Eat September 26, 2021 - 1:49 pm

That sounds delicious! The brown sugar on top is always a nice touch with whole wheat recipes. Thanks so much for the feedback, Rebecca.

Mary November 15, 2021 - 4:42 pm

I used a teaspoon of baking power, 1/2 cup of honey and added some walnuts. Delicious!

Beat Bake Eat November 15, 2021 - 6:58 pm

Nice! I’m glad you liked them, Mary. Thanks for leaving a comment.

Anonymous November 26, 2021 - 10:41 pm

Turned out very doughy and I could squish the muffins into a play dough consistency

Beat Bake Eat November 27, 2021 - 5:49 pm

Packed flour and under baked, perhaps?

Mary May 17, 2022 - 8:22 am

These are so yummy! I used half honey and half maple syrup and added a little bit of ground cloves. Will definitely make again.

Anonymous September 6, 2022 - 10:00 am

NO way would I use vegetable oil in ANYTHING! But the rest of the ingredients are definitely healthy. I will try this and substitute a healthier oil.

M September 24, 2022 - 1:52 pm

These came out great even with some omissions due to lack of ingredients/desire for less sugar. They have a great texture and bake up looking like the photo. I’ll definitely make them again. The changes I made were: leaving out the egg, using 1/3 cup honey and a little less than 1/3 cup syrup (not real maple, sadly), using 1 tsp of vanilla instead of 2 tsp, and substituting pumpkin spice for nutmeg. Next time I might try applesauce in place of the oil. So, even if you don’t have all the right ingredients, go ahead and give these a try. Mine did take a lot longer to bake but I did them in a toaster oven so that could have been why. They be even better with a streusel on top or swirled through!

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[…] to ring in the season is to cook something delicious! Maybe you have a favorite autumn baked good—pumpkin muffins always show up in my kitchen at some point by early […]

R. Webby April 11, 2023 - 5:27 pm

Delicious. Used half the sweetener (honey) and they still came out delicious. My 17 month old devours them. Highly recommend NOT using paper liners and just greasing the muffin tins. They pop right out. I found these REALLY stick to the paper liners.

Beat Bake Eat September 27, 2023 - 6:42 pm

Thanks for the tip! The batter is unusually sticky. I’m so happy your toddler loves them. I try my best to create whole wheat baking recipes that kids will enjoy just as much as adults.

Suzy September 28, 2023 - 10:32 am

I made this recipe using a combination of honey and maple syrup, and substituted nonfat Greek yogurt. The muffins are delicious and very moist. I did have to bake them for about 28 minutes to get the toothpick to come out clean. Great recipe!

Beat Bake Eat September 28, 2023 - 6:45 pm

Great! Love the honey-maple combo too. Maybe the nonfat yogurt had something to do with the extra baking time because they do contain additional ingredients to help maintain the texture.

Anonymous October 30, 2023 - 12:04 am

Best muffins ever! I used 1/4 c melted butter instead of the oil and they turned out great! Thank you for such a great recipe!

Beat Bake Eat October 30, 2023 - 10:31 am

You’re welcome! Happy you like them.

Mila November 7, 2023 - 10:59 pm

I’m planning on making these.
Would cottage cheese work instead of yogurt?

Beat Bake Eat November 8, 2023 - 10:55 am

Yes, I think it will work! But the consistency of cottage cheese is obviously different and it’s most likely going to affect the texture. Let me know how it turns out.