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Make your own copycat pumpkin cream cheese muffins at home! These taste just like the ones from Starbucks. They’re super moist and soft, filled with cozy spices, and have sweet cheesecake-like centers. Simple to make and perfect for fall!
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)
© Amy's Healthy Baking
Yields: 12 muffins
These super moist pumpkin muffins taste just like the irresistible ones from Starbucks! They’re full of cozy spices and a cheesecake-like filling. They’ll keep for at least four or five days (if not longer!) if stored in an airtight container in the refrigerator. And I highly recommend pairing them with my ultimate healthy pumpkin spice latte!
4.60 from 10 votes
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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
IMPORTANT MEASURING NOTE – READ BEFORE BEGINNING: Be very careful when measuring the flour! Use this method or a kitchen scale. (← That’s the one I own!) Too much flour will make your muffins dry, instead of moist and soft.
IMPORTANT FILLING NOTE – READ BEFORE BEGINNING: I don't recommend trying to dollop the filling in using measuring spoons and spatulas. That often doesn't push the filling down far enough into the batter, so the filling almost "rests" on the top of the muffins after they've finished baking, instead of being nestled inside. Use the makeshift "piping bag" method described in the instructions above, and remember to press the bag's opening down into the muffin batter itself before squeezing out the filling!
CREAM CHEESE NOTES + ALTERNATIVES: For the best results, use block-style cream cheese, rather than tub-style cream cheese. Neufchâtel (⅓-less fat) cream cheese, regular cream cheese, and fat-free cream cheese may all be substituted for the Greek yogurt cream cheese, as long as they have been well softened.
FLOUR ALTERNATIVES: Whole wheat pastry flour, regular whole wheat flour, or all-purpose flour may be substituted for the white whole wheat flour.
SPICE NOTES + ALTERNATIVE: For a stronger spice flavor, increase the cinnamon by up to an additional 1 teaspoon. (I love using this cinnamon because it tastes a little stronger and sweeter!)
If you prefer, 3 ½ teaspoons of pumpkin spice may be substituted for the cinnamon, nutmeg, and ginger.
BUTTER + COCONUT OIL ALTERNATIVES: Any neutral-tasting oil may be substituted for the unsalted butter or coconut oil. Stick-style vegan butter (I like this one and this one) will also work.
EGG WHITES NOTE: These muffins require 2 full egg whites. The whites contain the majority of the protein in eggs, and that protein is required to ensure the muffins maintain their shape and texture while cooling. If you prefer to use whole eggs, use 2 whole eggs AND reduce the milk by 1 tablespoon to compensate for the added liquid volume from the yolks.
LIQUID STEVIA NOTES + ALTERNATIVES: I highly recommend using the liquid stevia! It’s one of my favorite ingredients, and you’ll use it in all of these recipes of mine too. 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 recommend using the same one I do. I buy it online here because that’s the best price I’ve found.
If you prefer not to use liquid stevia in the muffin batter, substitute ½ cup (120mL) of pure maple syrup, honey, or agave AND omit the milk.
If you prefer not to use liquid stevia in the filling, then substitute 1½ tablespoons of this powdered stevia. Alternatively, use ¼ to ½ cup (48-96g) of sucralose, granulated sugar, or powdered sugar, depending on how sweet you'd like the filling to be. I do not recommend using a "regular" liquid sweetener (like pure maple syrup, honey, or agave) because it will make the filling too runny.
For a sweeter filling, increase the liquid stevia by ¼ to ½ teaspoon.
PUMPKIN PURÉE NOTES: Use regular canned pumpkin purée (also called 100% pure pumpkin). I don’t recommend substituting pumpkin pie mix! It contains added sugar, spices, and other ingredients, so it behaves differently in this recipe. I haven’t personally tried using homemade pumpkin purée, but I have a feeling it should work.
MILK ALTERNATIVES: Any milk may be substituted in place of the nonfat milk.
GLUTEN-FREE VERSION: For the gluten-free flour, I recommend the following blend: 1 cup (120g) millet flour, ½ cup (60g) tapioca flour, ½ cup (60g) brown rice flour, and 1 ½ teaspoons xanthan gum. Many store-bought gluten-free flour blends (I like this one from Bob's Red Mill) will work as well, if measured like this.
HOW TO STORE: Store the fully cooled muffins in an airtight container in the refrigerator. They should keep for at least four or five days, if not longer.
{gluten-free, clean eating, low fat, lower sugar, higher protein}
DID YOU MAKE THIS RECIPE?I'd love to hear what you think of it in a comment below! If you take a picture, tag @amys.healthy.baking on Instagram or use the hashtag #amyshealthybaking.
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!
