Last year, my mom and I stopped by a childhood friend’s house to see the mom and one of her three daughters, who was about four years younger than me. We carpooled for a few grades in both elementary and middle school, but after losing touch when everyone left town for college, Mom and I looked forward to saying hi.
When they opened the front door, we shared plenty of hugs all around, and the two ladies invited us in to sit and chat for a while in their living room. Before we settled back into the comfy sofa, the daughter showed me into the kitchen, where a batch of freshly baked treats cooled on the counter.
She was leaving on a road trip with her father extremely early the next morning, well before the sun rose and the birds started chirping, so she had whipped up some pumpkin cream cheese muffins for them to bring along for breakfast. She explained that they were a copycat of Starbucks’ seasonal treat, and she offered to send us home with a few.
As she packaged them up, she admitted, almost shamefully, that the muffins were nowhere near healthy. (She loves to bake as much as I do, and she’s made countless of my recipes from my blog!) I laughed and reassured her, “I’m a firm believer in ‘everything in moderation’ — even moderation itself, at times!”
When I recently dashed into Starbucks for a quick coffee pick-me-up, I spotted their autumn-themed muffins in the display case, which reminded me of my friend’s from that evening. With my pumpkin obsession, I knew I just had to create a healthier version, so here they are…
These healthy pumpkin cream cheese muffins! They have the same familiar flavors and super moist texture as the ones from Starbucks, along with the same creamy cheesecake-like centers. These homemade ones also have a protein boost — and they’re relatively simple to make too!
HOW TO MAKE THE BEST HEALTHY PUMPKIN CREAM CHEESE MUFFINS
To make these healthy copycat Starbucks pumpkin cream cheese muffins, you’ll start with white whole wheat flour. I know… That sounds rather contradictory, doesn’t it? But white whole wheat flour is made by finely grinding a special type of white wheat, whereas regular whole wheat flour comes from a heartier variety of red wheat. White whole wheat flour still has the same health benefits as regular whole wheat flour (like extra fiber!), but it has a lighter taste and texture, similar to that of all-purpose flour, which is perfect for letting the pumpkin flavor shine in these super moist muffins.
Tip: If you’d like to make these healthy pumpkin cream cheese muffins gluten-free, then check the Notes section of the recipe. I’ve included my top recommendations there!
Because they only contain 1 tablespoon of butter (or coconut oil, if you prefer!), the rest of these muffins’ tender texture comes from a combination of two ingredients: Greek yogurt and pumpkin purée. If you’ve been around my blog for a while, you know how much I love Greek yogurt! It adds the same moisture as extra butter or oil for a fraction of the calories, and it gives your healthy copycat pumpkin cream cheese muffins a protein boost too.
As for the pumpkin, you need regular ol’ pumpkin purée. It’s also called 100% pure pumpkin and canned pumpkin. Don’t substitute canned pumpkin pie mix! That contains refined sugar and other ingredients, which makes it behave differently in baking recipes compared to regular pumpkin purée.
You’ll sweeten the muffins with another one of my favorite ingredients: liquid stevia. Stevia is a plant-based, no-calorie sweetener that’s clean eating friendly, and it’s highly concentrated. You just need 1 ½ teaspoons for the muffin batter! This is the kind that I buy because I love its sweet flavor and don’t detect any strange aftertastes like some other stevia products have. You can find it at many health-oriented grocery stores, but I buy mine online here because that’s the best price I’ve found. (And you’ll use it in all of these recipes of mine too!)
Tip: Many stevia brands and products have different sweetness levels, so they’re not necessarily 1-for-1 substitutes for each other. For the best results, I highly recommend using the same liquid stevia that I do!
HOW TO FILL THE CENTERS OF PUMPKIN CREAM CHEESE MUFFINS
For the sweet cream cheese centers of the copycat Starbucks pumpkin muffins, you’ll mix together a combination of Greek yogurt cream cheese and Greek yogurt, along with a hint of vanilla and more liquid stevia. I found my Greek yogurt cream cheese at Safeway (their own Lucerne brand), and many Walmart stores carry this brand.
Tip: If you can’t find Greek yogurt cream cheese, then Neufchâtel cream cheese (aka ⅓-less fat cream cheese) is a fantastic substitute!
To add the cream cheese mixture to muffins before baking them, transfer it to a zip-topped plastic bag, cut off one corner, and pipe it into the center portion of the batter. Super easy — plus using the bag makes clean-up a breeze!
Tip: I don’t recommend trying to dollop the mixture in using measuring spoons and spatulas. That can be quite messy… And that method often doesn’t push the filling down far enough into the batter, so it almost “rests” on the top of the muffins after they’ve finished baking, instead of being nestled inside. Use the makeshift “piping bag” method above, and remember to press the bag’s opening down into the muffin batter itself before squeezing out the filling!
FAQS ABOUT HEALTHY PUMPKIN CREAM CHEESE MUFFINS
Are these copycat Starbucks pumpkin cream cheese muffins sugar-free, gluten-free, clean eating, low fat, or low calorie?
Yes — to all of the above! These healthy pumpkin muffins are sugar-free, clean eating, low fat, and low calorie (compared to the original ones!). I also included my top gluten-free recommendations in the Notes section of the recipe!
I can’t find that flour. Can I use a different one?
You sure can! Whole wheat pastry flour is a fantastic substitute. Regular whole wheat flour and all-purpose flour both work too!
What about a different sweetener?
There are a few others that will work! I’ve shared my recommendations in the Notes section of the recipe.
Can I substitute pumpkin spice?
Absolutely! Use 3 ½ teaspoons of pumpkin spice to replace the cinnamon, nutmeg, and ginger.
Where do you find Greek yogurt cream cheese? Is there an alternative?
It’s sold right next to the regular cream cheese! I’ve had good luck at Safeway, Vons, and Walmart. Many other grocery stores also carry Greek yogurt cream cheese. If you can’t find it, then Neufchâtel (⅓-less fat) cream cheese is the best alternative. Regular cream cheese and fat-free cream cheese also work. Whatever option you use, make sure it’s (a) block-style and (b) well softened for the best results!
Could I press pepitas (pumpkin seeds) into the tops, just like Starbucks does?
That should work! I’m not a fan of nuts or seeds in my muffins and always pick them off to eat separately… Which is why I didn’t include any in my homemade version. But if you’d like to add some to make your copycat pumpkin cream cheese muffins more authentic, feel free!
How should I store these healthy pumpkin cream cheese muffins? And how long do they last?
Store them in an airtight container in the refrigerator. (Because of the pumpkin and its moisture, they go bad really quickly if left at room temperature.) They should keep for at least four or five days, if not longer!
Now… Who needs Starbucks when you have these muffins and a healthy homemade pumpkin spice latte around? 😉
And when you make your own, remember to snap a picture and share it on Instagram using #amyshealthybaking and tagging @amyshealthybaking IN the photo itself! (That guarantees I’ll see your picture! 🙂 ) I’d love to see your healthy pumpkin cream cheese muffins!
Healthy Pumpkin Cream Cheese Muffins (Starbucks Copycat)
Ingredients
FOR THE FILLING
- 6 tbsp (90g) plain nonfat Greek yogurt
- 6 tbsp (84g) Greek yogurt cream cheese, softened
- ½ tsp liquid stevia (or adjusted to taste)
- ¼ tsp vanilla extract
FOR THE MUFFINS
- 2 cups (240g) white whole wheat flour or gluten-free* flour (measured like this)
- 1 tbsp (8g) ground cinnamon
- ¼ tsp ground nutmeg
- ¼ tsp ground ginger
- 1 ½ tsp baking powder
- ½ tsp baking soda
- ½ tsp salt
- 1 tbsp (14g) unsalted butter or coconut oil, melted and cooled slightly
- 2 large egg whites, room temperature
- 1 ½ tsp vanilla extract
- 1 ½ tsp liquid stevia
- ¼ cup (60g) plain nonfat Greek yogurt
- 1 cup (244g) pumpkin purée, room temperature (not pumpkin pie mix!)
- ½ cup (120mL) nonfat milk
Instructions
- Preheat the oven to 350°F, and lightly coat 12 muffin cups with nonstick cooking spray.
- To prepare the filling, beat the Greek yogurt and Greek yogurt cream cheese with a mixer until smooth and creamy. Add in the liquid stevia and vanilla. Beat until fully incorporated. Transfer to a zip-topped plastic bag.
- To prepare the muffin batter, whisk together the flour, cinnamon, nutmeg, ginger, baking powder, baking soda, and salt in a medium bowl. In a separate bowl, whisk together the butter, egg whites, vanilla, and liquid stevia. Stir in the Greek yogurt, mixing until no large lumps remain. Stir in the pumpkin purée. Alternate between adding the flour mixture and milk, beginning and ending with the flour mixture, and stirring just until incorporated. (For best results, add the flour mixture in 3 equal parts.)
- Evenly divide the batter between the prepared muffin cups. Cut the corner off of the zip-topped bag with the filling, and pipe the filling into the center of each muffin cup’s batter. (It’s okay if the filling sticks up a little over the top of the batter. The batter will rise around its sides some as it bakes.) Bake at 350°F for 20-23 minutes or until the pumpkin parts of the tops feels firm to the touch and a toothpick inserted into the pumpkin part comes out clean or with a few crumbs attached. Cool in the muffin cups for 10 minutes before transferring to a wire rack.
Notes
View Nutrition Information + Weight Watchers Points
You may also like Amy’s other recipes…
♡ Healthy Pumpkin Cake with Cream Cheese Frosting
♡ Healthy Pumpkin Cheesecake Bars
♡ Healthy Pumpkin Pancakes
♡ Healthy Pumpkin Cinnamon Rolls
♡ Healthy Pumpkin Pie Protein Overnight Oats
♡ Healthy Chocolate Chip Pumpkin Bran Muffins
♡ Healthy Chocolate Chip Pumpkin Scones
♡ …and the rest of Amy’s healthy pumpkin recipes!
I’m sorry, I followed your recipe to the t and they came out salty and not sweet at all, very dense. I gave up and drowned them in sugar as a final attempt to salvage all the ingredients. Very disappointed. Don’t waste your time or ingredients.????
I really appreciate your interest in my recipe! That sounds really disappointing and not like how these muffins should turn out at all, so I’d love to work with you to figure out what happened! 🙂 Did you use the same stevia that I did? Did you make any modifications to the recipe, including those listed in the Notes section? Did the texture of the insides of your muffins look the same as my muffins in the photo directly above the recipe? Once I know your answers to all of those questions, then I’ll have a much better idea of what happened with your batch!
I really wish i could find a recipe without stevia. I don’t know how people can eat that stuff. It doesn’t taste sweet at all to me. It taste like crushed aspirin. Would these work if I subbed it with maple syrup? Thanks for your help! -Nicole
I’m thinking about making this for the holidays. Do you have the nutritional information available? I’d like to make a keto-friendly version and I think what you have may be pretty close.
The full nutrition information is available directly underneath the recipe box! I know it can be easy to miss. 😉 I’d love to hear what you think if you try making these muffins, Edie!
Made this recipe but used Swerve instead of Stevia. They were delicious!
I’m so glad you enjoyed these muffins, Sharon! Thank you for taking the time to let me know — that really means a lot! 🙂
Hi Amy,
I’m so glad to have found your website and I love this recipe in particular! I personally prefer to almost double the cream cheese filling and cut the sweetness by reducing stevia, but the original recipe works fantastically and the muffins come out moist and fluffy. Just want to say thank you and please keep posting!
Best,
Eva
You’re just the sweetest, Eva! Thank you so much for your kind comment. It truly means a lot that you’re enjoying my website and recipes, and it means even more that you’d take the time to let me know! 🙂 I’m so glad you liked these muffins. I’ll never turn down extra cream cheese filling either — I think that’s a delicious idea! 😉 I can’t wait to hear which recipe of mine you pick to try next, once all of your muffins have disappeared!
Hi! The recipe was good but my cream cheese filling oozed out a little bit while cooking…but once the muffins cooled, the filling recessed back into the muffin and left big holes in the tops hahaha. I’m trying to figure out what I need to do so it doesn’t happen next time.
It means a lot that you tried my recipe Christina! I’m happy to help figure that out. 🙂
Did you make any substitutions or modifications to the recipe, including those listed in the Notes section? Especially for the filling?
After mixing together the filling, did you notice lots of air bubbles in it, by any chance?
What brands of yogurt, cream cheese, and liquid stevia did you use?
When you filled the muffin batter with the cream cheese mixture, did you use a zip-topped bag with the corner cut off, like in the instructions? Or did you use a spoon or something else instead? (Some readers have done that, so I just like to double check!)
If you used the zip-topped bag, how far into the batter did you insert it before beginning to squeeze out the cream cheese mixture?
Did the muffin batter rise up around the sides of the filling while the muffins baked?
How was the flavor and texture of the muffin part?
I know I just asked a LOT of questions, but I’ll have a much better idea of the potential culprit once I know your answers to all of them!
I don’t have liquid stevia so for the muffin batter, I used honey and omitted the milk. For the filling I used 6 tbs of sugar, i thought it was plenty sweet with just 6.
I didn’t notice air bubbles.
I didn’t have Greek yogurt so I used whole milk regular yogurt. I also noticed you recommended block cream cheese but I didn’t have that so I used cream cheese from a tub.
I used the zip lock bag method.
Here’s where I think I might have messed up lol. I inserted the cream cheese filling very deep into the muffin..I noticed your pretty pictures have a nice area of filling more towards the top.
The muffin batter did rise up around the cream cheese a little but the cream cheese definitely came up a little further…the actual muffin texture was soft and moist, very good.
Thank you for sharing this additional information, Christina! If you inserted the cream cheese filling very deep into the muffin batter, that was actually a good thing. If you didn’t, your filling would’ve oozed and seeped out even more!
The substitutions that you made in the cream cheese filling actually made a difference and would have contributed to the issue that you experienced.
First, regular yogurt is usually thinner and looser than Greek yogurt. By using that in the filling, that added more liquid volume and made the cream cheese mixture thinner and more runny.
Second, tub-style cream cheese has a similar effect. It’s usually softer and a bit looser than block-style, which also would’ve made your cream cheese filling thinner and more runny.
I designed the filling to be thick and hold its shape so it would stay put in the center of the muffins while baking. A filling that’s looser and more runny definitely would’ve seeped and oozed outward in comparison! 😉
So if you’d like to make these muffins again in the future, I’d recommend using Greek yogurt and block-style cream cheese for the filling. If you’re okay using stevia, then that will also help reduce its potential to ooze and seep out even more. (I buy my stevia online at the link I’ve provided in the recipe!) Those things should help your muffins turn out much better!
Cool I’ll try those things next time then. Thank you so much for your help!!!
It’s my pleasure, Christina! I’m happy to help! 🙂
I have made these 2 times this week and they are great! The first ones stuck to the bottom of the papers a little, but were a huge hit! The second ones I added a little more pumpkin and didn’t use as much sweeter in the filling, they were also really good! The first set was more cupcake like and the second set was more of a muffin in my opinion. Either way, this recipe is definitely one that I will use again!
I’m so glad you enjoyed these muffins, Brook! That’s such a huge compliment that you think you’ll make them again. I’m so honored — thank you for taking the time to let me know! 🙂
Hello! I was thinking of making this recipe, and I was wondering if I could add protein powder to the muffins to add even more protein. Do you recommend doing this, and if so how would I go about it?
Keep up the great work!
We really appreciate your kind words and interest in our recipe, Kyli! We actually have an entire FAQ page dedicated to baking with protein powders (Protein Powder FAQ). Perhaps that might be useful?
Because many protein powders behave differently in baking recipes, we can’t predict the results of adding or substituting them in our recipes that don’t explicitly call for them. However, we actually do have some protein muffin recipes! Maybe those would be of interest? It might be easier to follow one of those instead of modifying this one, but you’re more than welcome to experiment with substituting protein powder for some of the flour in these pumpkin muffins too! We just can’t personally vouch for the results. 😉
We also have even more recipes that use protein powder as an ingredient here. Just in case you might be interested in trying something like protein cookies, energy bites, or snack bars too!
We’d love to hear how your muffins turn out if you end up making them — or any of our other recipes!