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These healthy pumpkin cream cheese muffins are pure fall magic! We’ve taken the classic Starbucks favorite and made it lighter without losing any of the flavor. Soft, fluffy, and bursting with warm pumpkin spice, each muffin has an incredible cream cheese filling that tastes indulgent while being perfectly lightened up.
The best part? These pumpkin cream cheese muffins come together quickly with simple ingredients, making them the ultimate fall treat. They’re cozy, flavorful, and perfect with a cup of coffee or as a sweet treat. This will be your new favorite fall muffin, guaranteed!
For more delicious pumpkin muffins, try our healthy pumpkin spice muffins, pumpkin oat muffins, and pumpkin chocolate chip muffins next! And if you love the flavors of pumpkin and cream cheese, don’t miss our pumpkin cream cheese cookies!
Why You Will Love Pumpkin Cream Cheese Muffins
- Healthier Twist: These muffins are lightened up with applesauce and light cream cheese, with the option to use a sugar substitute. There’s no oil or butter in this recipe, but they’re still incredibly moist!
- Starbucks Copycat Flavor: You get all the cozy fall flavors of the classic Starbucks pumpkin cream cheese muffins, made lighter and fresher at home.
- Cozy Flavor & Fluffy Texture: These muffins have a soft and fluffy texture. They have a rich pumpkin flavor that pairs well with the sweet and tangy cream cheese filling.
- Easy to Make: There aren’t any complicated steps or fancy equipment needed to make this recipe. We’ve simplified the process!
“Just made the pumpkin cream cheese muffins! YUM!!! The muffins were so moist! And the sweetness was just right – not over powering. Definitely a nice healthy treat to have with a cup of coffee or hot tea!”
– valli
Ingredients Needed
- Flour: The base of these muffins is all-purpose flour.
- Pumpkin Pie Spice: Adds that warm and cozy fall flavor!
- Leavening Agents: Baking powder and baking soda help the muffins rise and stay fluffy.
- Salt: Enhances all the flavors.
- Sweetener: Sweeten these muffins with brown sugar or a 1:1 sugar-free sweetener such as brown monk fruit.
- Pumpkin Puree: This recipe utilizes a full can of pumpkin puree!
- Eggs: Two whisked eggs help bind everything together.
- Applesauce: Unsweetened applesauce keeps the muffins moist without needing oil or butter.
- Vanilla Extract: A splash of vanilla extract for flavor.
- Cream Cheese Filling: Make the cream cheese filling with softened cream cheese, sugar or a sugar-free sweetener, and vanilla extract.
Find the full measurements in the recipe card below.
Substitutions & Variations
- Cream Cheese Options: You can use fat-free, light, or regular cream cheese for this recipe.
- WW-Friendly: To make these muffins WW-friendly, use light or fat-free cream cheese and a sugar-free sweetener such as monk fruit.
- Gluten-Free Option: Swap the flour with a 1:1 gluten-free all-purpose flour blend.
- Optional Topping: You can sprinkle pumpkin seeds or a dash of cinnamon sugar on top before baking.
How To Make Pumpkin Cream Cheese Muffins
Step 1: In a small bowl, mix the softened cream cheese, sweetener, and vanilla extract until smooth. Set aside.
Step 2: In a large bowl, mix the flour, pumpkin pie spice, baking powder, baking soda, and salt.
Step 3: In a separate bowl, whisk the eggs. Then add the pumpkin puree, brown sugar or sugar-free sweetener, applesauce, and vanilla extract. Whisk until combined.
Step 4: Pour the wet ingredients into the dry ingredients a little at a time, stirring until just combined. Don’t over-mix.
Step 5: Line a non-stick muffin tin with parchment paper liners or spray it with oil.
Step 6: Pour batter into each muffin cup.
Step 7: Scoop slightly less than 1 tablespoon of the cream cheese mixture into the center of each muffin. A 1-tablespoon cookie scoop works great for this.
Step 8: Bake the muffins at 350°F for 20-25 minutes, or until a toothpick inserted into the muffin comes out clean. Once done, let the muffins slightly cool, and enjoy!
Shawna’s Expert Tips
- Use Pumpkin Puree: Make sure to use pumpkin puree, not pumpkin pie filling, as pie filling often has added sugar and spices.
- Soften the Cream Cheese: Let it come to room temperature so it’s easy to mash with the vanilla and sweetener before adding it to each muffin.
- Even Scoop: Add slightly less than a tablespoon of the cream cheese filling to each muffin. Using a cookie scoop makes it quick and even.
- Don’t Over-Mix the Batter: Mix the batter just until combined so the muffins stay light and fluffy.
Serving Suggestions
Enjoy your pumpkin cream cheese muffins warm with a hot cup of coffee or tea. They’re delicious with a classic latte, chai latte, pumpkin chai latte, or even a pumpkin spice latte if you’re craving all the fall flavors. They make the perfect grab-and-go breakfast, snack, or sweet fall treat when you’re craving Starbucks flavors without leaving your kitchen!
Frequently Asked Questions
How Long Do Pumpkin Cream Cheese Muffins Last?
You can store leftover homemade pumpkin cream cheese muffins in an airtight container in the refrigerator for 3-4 days.
Can You Freeze Pumpkin Cream Cheese Muffins?
Yes, you can freeze these pumpkin cream cheese muffins in an airtight freezer-safe container for up to 2 months.
More Healthy Muffin Recipes to Try!
- Healthy Pumpkin Spice Muffins
- Apple Cinnamon Muffins
- Apple Oat Muffins
- Gingerbread Muffins
- Chocolate Cranberry Muffins
If you try this recipe, please be sure to leave us a comment and star rating, ★★★★★, letting us know how it turns out for you.
HEALTHY PUMPKIN CREAM CHEESE MUFFINS
Ingredients
For the Pumpkin Muffins:
- 1 ¾ cups all-purpose flour
- 2 teaspoons pumpkin pie spice
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- 1/2 teaspoon salt
- 3/4 cup brown sugar or 1:1 sugar-free sweetener such as brown monk fruit
- 1, 15-ounce can of pumpkin puree
- 2 eggs, whisked
- 1/4 cup unsweetened applesauce
- 1 teaspoon vanilla extract
For the Cream Cheese Filling:
- 6 ounces light cream cheese, softened to room temperature
- 3 tablespoons sugar or a 1:1 sugar substitute such as monk fruit
- 1/2 teaspoon vanilla extract
Instructions
- Make the cream cheese filling: In a small bowl, mix the softened cream cheese, sweetener, and vanilla extract until smooth. Set aside.
- Mix the dry ingredients: In a large bowl, mix the flour, pumpkin pie spice, baking powder, baking soda, and salt.
- Mix the wet ingredients: In a separate bowl, whisk the eggs. Then add the pumpkin puree, brown sugar or sugar-free sweetener, applesauce, and vanilla extract. Whisk until combined.
- Combine wet and dry: Pour the wet ingredients into the dry ingredients a little at a time, stirring until just combined. Don’t over-mix.
- Prepare the muffin tin: Line a non-stick muffin tin with parchment paper liners or spray it with oil.
- Fill the cups: Pour batter into each muffin cup, filling about ⅔ of the way full.
- Add the cream cheese filling: Scoop slightly less than 1 tablespoon of the cream cheese mixture into the center of each muffin. A 1-tablespoon cookie scoop works great for this.
- Bake: Bake the muffins at 350°F for 20-25 minutes, or until a toothpick inserted into the muffin (not the cream cheese center) comes out clean. Once done, let the muffins slightly cool, and enjoy!
Video
Notes
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Just made the pumpkin cream cheese muffins! YUM!!! The muffins were so moist! And the sweetness was just right – not over powering. Definitely a nice healthy treat to have with a cup of coffee or hot tea!
I’m so happy you enjoyed the pumpkin cream cheese muffins! It’s wonderful to hear they were moist and had just the right amount of sweetness. Thank you so much for taking the time to leave a review.
PS – My 18-month old grandbaby enjoyed the muffins too! So I made a second batch using mini-muffins pans so that he would have his own perfectly sized muffins!!
Hi Valli, that’s absolutely wonderful to hear! We love that your grandbaby enjoyed them too. How sweet! Making mini muffins just for him is such a great idea. Thank you so much for sharing that with us, it truly warms our hearts!
Wow! I’ve made several muffin recipes on this blog but these are my favorite. The top is a little messy with the cream cheese but the texture and flavor is perfection. I have celiac disease so I used GF Jules gluten free flour & brown sugar.
Hi Heather, thank you so much! I’m so glad you loved these pumpkin cream cheese muffins! That’s great to know they turned out perfectly with GF Jules flour, that’s so helpful for others too! Thank you so much for leaving a review. 🙂
I made these muffins with brown Monk Fruit sweetener and fat-free cream cheese. I half expected they wouldn’t be as good without the extra fat and sugar, but they turned out perfect. They have just the right amount of sweetness to have with my coffee in the morning. I will definitely make these again!
Hi Patri, I’m so glad the pumpkin cream cheese muffins turned out perfect for you! Using brown monk fruit sweetener and fat-free cream cheese is such a great swap, and it’s great to know the muffins still had the right amount of sweetness. They sound like the perfect treat to enjoy with your morning coffee. Thank you for sharing your experience, I’m so happy you’ll be making them again!