These Protein Pumpkin Cream Cheese Muffins are spiced pumpkin protein muffins with a sweetened cream cheese center, inspired by the Starbucks classic, with 8g of protein per muffin.
Save This Recipe to Your Email!
We'll email this recipe to you, so you can come back to it later!
Every fall I get a craving for the Starbucks pumpkin cream cheese muffin, and this year I finally made my own version instead of heading out to get one.
The Starbucks pumpkin cream cheese muffin is a genuine fall favorite, and for good reason — warm pumpkin spice muffin wrapped around a sweet, tangy cream cheese center is a hard combination to beat. This version leans on the same idea, but with whole wheat pastry flour and a couple scoops of protein powder mixed into the batter, so it holds up better as an actual breakfast instead of just a coffee shop treat.
Most protein muffin recipes skip a cream cheese filling entirely, since it adds extra sugar and fat to work around. And most cream cheese muffin recipes aren’t trying to be a protein source at all. This one does both — you still get that filling you’d expect from the original, just with 8g of protein per muffin working in your favor too.
If you’re leaning into pumpkin protein season, this is just one of a few ways I do it. My Pumpkin Protein Muffins are this same base recipe without the cream cheese filling, swapped for chocolate chips instead, if you want something a little simpler.
For breakfasts that don’t involve the oven, my Protein Pumpkin Chia Pudding and High Protein Pumpkin Overnight Oats are both good no-cook options for busier mornings, and my Protein Pumpkin Baked Oatmeal is another one in the regular rotation this time of year, too.
Jump to:
What Do Protein Pumpkin Cream Cheese Muffins Taste Like?
Warm pumpkin spice throughout the muffin — cinnamon, ginger, nutmeg, and clove all doing their thing — with a tangy-sweet cream cheese center that cuts through the spice. It’s not overly sweet overall, closer to a bakery muffin than a dessert, which is part of what makes it work as breakfast.
Why You Will Love These Pumpkin Cream Cheese Muffins
- 8g of protein per muffin: these high protein pumpkin muffins are a more filling take on the classic.
- Tastes like the Starbucks version: without needing a coffee shop trip to get one.
- Whole wheat pastry flour: adds a bit more substance than an all-purpose-only muffin.
- Freezer-friendly: make a batch and pull muffins out as needed.
- A real cream cheese filling: not just a glaze or swirl — an actual center you bite into.
- Cheaper than Starbucks: a whole batch costs less than a few muffins from the coffee shop.
Ingredients Needed
- Whole wheat pastry flour: the base of the batter, and it also helps the cream cheese filling hold together while baking.
- Protein powder: plain or vanilla both work — this is what boosts the protein content.
- Cinnamon, ginger, nutmeg, and cloves: the warm pumpkin spice blend.
- Canned pumpkin puree: real pumpkin flavor and moisture — make sure it’s puree, not pie filling.
- Coconut sugar: sweetens the batter (brown sugar works too).
- Large eggs: bind everything together.
- Avocado oil: keeps the muffins moist.
- Plain Greek yogurt: adds moisture and a little extra protein.
- Vanilla extract: rounds out the flavor in both the batter and the cream cheese filling.
- Cream cheese: the block kind at room temperature, for the tangy, sweet center.
- Granulated sugar: sweetens the cream cheese filling without changing the color.
Substitutions & Variations
- Coconut sugar swap: brown sugar is a 1:1 substitute in the muffin batter.
- Dairy-free: a dairy-free cream cheese alternative can stand in for the filling.
- Chocolate chips instead of filling: if you’d rather skip the cream cheese step, my Pumpkin Protein Muffins use this same base with chocolate chips folded in instead.
- Gluten-free: a 1:1 gluten-free flour blend works in place of the whole wheat pastry flour in both the batter and filling.
Instructions
- Step 1: Get your oven preheating to 375°F and line a 12-count muffin tin with liners.
- Step 2: Stir together the flour, protein powder, cinnamon, ginger, nutmeg, cloves, and baking soda in one bowl, then set it aside.
- Step 3: Whisk the pumpkin, coconut sugar, eggs, oil, Greek yogurt, and vanilla together in a second bowl, until the yogurt is fully worked in and no clumps remain.
- Step 4: Pour the dry ingredients into the wet ingredients and stir until just combined, then set the batter aside.
- Step 5: Make the filling by stirring together the room-temperature cream cheese, sugar, flour, and vanilla until smooth.
- Step 6: Divide the muffin batter evenly among the 12 muffin cups. Scoop a little less than a tablespoon of the cream cheese filling into the center of each one, pressing it in gently.
- Step 7: Bake for 21-23 minutes, until a toothpick inserted into the muffin part (not the filling) comes out clean. Let them cool before serving.
Recipe Success Tips
- Use room temperature cream cheese: cold cream cheese won’t mix smoothly and can leave lumps in the filling.
- Don’t overmix the batter: stir just until the flour disappears — overmixing leads to denser muffins.
- Press the filling in gently: you want it centered in the muffin, not sitting right on top or sinking all the way to the bottom.
- Check doneness in the muffin, not the filling: the cream cheese center will look soft even when the muffin itself is fully baked, so test the toothpick in the batter portion.
- Let them cool before storing: this helps the cream cheese filling set up properly.
Storage Directions
Because of the cream cheese filling, store these muffins in the refrigerator in an airtight container for up to 3 days.
For longer storage, they freeze well for up to 3 months — thaw overnight in the fridge or warm briefly in the microwave.
Are These Protein Pumpkin Muffins Healthy?
Yes — this is a genuinely more filling take on the classic pumpkin cream cheese muffin, with 8g of protein per muffin thanks to the protein powder and Greek yogurt in the batter.
A typical bakery-style pumpkin cream cheese muffin doesn’t offer much protein at all, so this version holds up better as an actual breakfast rather than just a treat with your coffee.
Total nutritional content per serving is:
- Calories: 237 calories
- Carbohydrates: 29 grams
- Protein: 8 grams
- Total Fat: 11 grams
- Sodium: 242 mg
- Fiber: 3 grams
*This nutritional information is an estimate and calculated based on the ingredients used to create the recipe. The nutritional value of your ingredients may differ slightly. Furthermore, this food is not intended to prevent, diagnose, cure, or treat any disease.
Pricing Info
This recipe costs about $8.39 total, or $0.70 per muffin. That’s considerably cheaper than buying a single pumpkin cream cheese muffin at a coffee shop, which typically runs $4-5 apiece — this batch of 12 costs less than four store-bought muffins combined.
This is what I personally paid to make this recipe:
- 1 ¼ cups + 2 tsp whole wheat pastry flour: $0.34
- ½ cup protein powder: $1.76
- 2 tsp cinnamon: $0.04
- 1 ½ tsp baking soda: $0.02
- ½ tsp ground ginger: $0.02
- ½ tsp ground nutmeg: $0.03
- ¼ tsp ground cloves: $0.01
- 15 oz canned pumpkin puree: $2.23
- ¾ cup coconut sugar: $0.63
- 2 large eggs: $0.90
- ¼ cup avocado oil: $0.89
- ¼ cup plain Greek yogurt: $0.25
- 2 ¼ tsp vanilla extract: $0.09
- 6 oz cream cheese: $1.17
- 1 ½ tbsp granulated sugar: $0.01
The total comes out to be around $8.39 or roughly $0.70 per muffin!
FAQs
The flavor and cream cheese center are inspired by the same idea, but this version swaps in whole wheat pastry flour and protein powder, bringing 8g of protein to the table that the original doesn’t offer.
No — the pumpkin, spices, and cream cheese filling are all flavorful enough to cover any protein powder taste. Using a vanilla or plain protein powder rather than a strongly flavored one also helps keep it undetectable.
Yes. Let them cool completely, then store in a freezer-safe bag or container for up to 3 months. Thaw overnight in the fridge or warm briefly in the microwave before eating.
No — all-purpose flour works as a 1:1 substitute if that’s what you have on hand. Whole wheat pastry flour just adds a bit more fiber and substance to the muffin.
Other Protein Muffin Recipes
Tried this recipe? Please leave a ⭐⭐⭐⭐⭐ rating in the comments below! I would really appreciate your feedback!
Recipe
Protein Pumpkin Cream Cheese Muffins (Better Than Starbucks)
Equipment
Ingredients
Protein Pumpkin Muffins:
- 1 ¼ cups whole wheat pastry flour
- ½ cup protein powder plain, vanilla, or chocolate
- 2 tsp cinnamon
- 1 ½ tsp baking soda
- ½ tsp ground ginger
- ½ tsp ground nutmeg
- ¼ tsp ground cloves
- 15 oz canned pumpkin puree (not pumpkin pie filling)
- ¾ cup coconut sugar or brown sugar
- 2 large eggs
- ¼ cup avocado oil
- ¼ cup plain Greek yogurt
- 2 tsp vanilla extract
Cream Cheese Filling:
- 6 oz cream cheese room temperature
- 1 ½ tbsp granulated sugar
- 2 tsp whole wheat pastry flour
- ¼ tsp vanilla extract
Instructions
- Preheat your oven to 375° and line a 12-count muffin tin.
- In a medium bowl, mix together the flour, protein powder, cinnamon, ginger, nutmeg, cloves, and baking soda. Set aside.
- In a separate bowl, whisk together pumpkin, coconut sugar, eggs, oil, Greek yogurt, and vanilla. Whisk until no clumps of yogurt remain.
- Add the dry ingredients and stir until just combined. Set aside.
- Make the cream cheese filling by stirring together the room-temperature cream cheese, granulated sugar, flour, and vanilla until smooth and combined. Set aside.
- Divide the batter evenly between 12 muffins. Scoop a little less than 1 tbsp of the cream cheese mixture onto the center of each muffin, then press them into the batter slightly.
- Bake for 21-23 minutes or until a toothpick inserted in the center comes out clean. Allow to cool, then serve. Store in the fridge for up to 3 days or the freezer for up to 3 months.
Video
Nutrition
If you end up making this and loving it, take a photo and tag me on Instagram! I’d love to see your versions of my recipes! And feel free to rate it down below in the comment section. I would really appreciate it!
xoxo Megan
Leave a Reply