IIf you love the pumpkin cream cheese muffins from Starbucks, you are going to love this homemade version even more. These muffins start with a soft, warmly spiced pumpkin batter and get stuffed with a sweet, tangy cream cheese filling right in the center of every single one. They bake up moist and tender with a golden domed top, and they taste like a real bakery treat made with simple pantry ingredients you likely already have on hand. Whether you want a cozy breakfast, an afternoon snack, or something special for a fall brunch table, this recipe is easy enough for a beginner and reliable enough to make again and again all season long.

Why this is the best Pumpkin Cream Cheese Muffins recipe
It's an easy homemade version of the Starbucks favorite. These pumpkin cream cheese muffins have all the flavors you love in the coffee shop version, but you can make a whole batch at home whenever the craving hits.
These pumpkin cream cheese muffins are soft, moist, and full of pumpkin spice flavor. Pumpkin puree keeps the muffins tender while cinnamon and warm fall spices give them that classic pumpkin flavor without overpowering the sweet cream cheese center.
The cream cheese filling makes these muffins extra special. Every muffin has a rich, creamy cheesecake-like center that pairs beautifully with the lightly spiced pumpkin muffin.

These cream cheese pumpkin muffins are great for breakfast, brunch, dessert, or an afternoon snack. Make a batch for a cozy fall weekend, serve them for Thanksgiving breakfast, or grab one with your morning coffee when you want a bakery-style treat without a trip to Starbucks.
What you'll need to make the best Pumpkin Cream Cheese Muffin Recipe
Equipment
- Electric mixer - This is to beat the cream cheese mixture and make it nice and creamy without lumps.
- Scoop set - You will use a medium scoop to portion out the muffins so that they're all the same size.
- Muffin tin - To cook the muffins.
- Cupcake wrappers - So that your muffins don't stick to the muffin pan. If you don't have muffin cups, make sure you spray the wells of the muffin pan generous with cooking spray or grease them with butter.

See the printable recipe card at the bottom of the page for all measurements and nutritional information.
Ingredients
- Flour: We prefer all purpose flour, but a cup-for-cup gluten-free baking mix will also work.
- Sugar: A mixture of granulated white sugar and brown sugar works best.
- Baking Powder: Do not reduce; this is what allows the muffins to rise.
- Pumpkin Pie Spice: If you can't find pumpkin pie spice, feel free to sub in 1 teaspoon cinnamon, ¼ teaspoon nutmeg, and a pinch of cloves; it won't taste exactly the same, but it will still turn out delicious.
- Pumpkin Puree: Be sure to use pumpkin puree, NOT pumpkin pie mix which is already spiced and generally unpleasant in my opinion.
- Cream Cheese: For best results, use full fat cream cheese and make sure it is softened to room temperature before using. The best way to do this is to sit it on the counter a few hours before you need it, but if you forget to do that, you can microwave it in 20-30 second bursts until it is soft enough to work with.
- Milk: Whole milk and almond milk will both work.
- Butter: Butter and imperial margarine sticks will both work. We used unsalted butter but the amount of salt is negligible and won't impact your muffins even if you use salted.
How to make easy Pumpkin Cream Cheese Muffins
- Preheat the oven to 350℉ and line the muffin tin with cupcake liners.
- Whisk together the flour, sugars, baking powder, and pumpkin pie spice in a large bowl.
- Make a well in the center of the dry ingredients and stir in the pumpkin and vegetable oil with a spatula, ensuring there are no dry spots in the batter, but do not overmix. Set aside.

- Beat together the softened cream cheese, powdered sugar, milk, and vanilla bean paste in a medium bowl until smooth and creamy. Set aside.


- Blend together the sugar, flour, and cinnamon in a small bowl with a fork, then stir in the melted butter until there are no dry spots. Set aside.

- Assemble the muffins by scooping 1 tablespoon of muffin batter,

1 tablespoon of cream cheese mixture,
2 tablespoons of muffin batter,
and then a sprinkle of topping into each muffin liner in the muffin tin.
- Bake muffins for about 20-23 minutes, or until a toothpick comes out clean or with only cream cheese mixture or crumbs.

Repeat the last 2 steps with the remaining batter and mixtures. - Allow to cool for 10 minutes in the muffin pan, then transfer to fully cool on a wire rack.

Cook's Tips
You can spritz the cupcake liners with cooking spray prior to adding the batter, to prevent the muffins from sticking after baking.
Feel free to omit the buttery topping, or simply add a mixture of cinnamon and sugar on top before baking. 1 tablespoon cinnamon to 3 tablespoons white or brown sugar.
If you prefer not to bake the cream cheese, you can certainly bake the muffins first by adding 4 tablespoons (¼ cup) of the batter to each muffin liner, then add the topping if you wish. Bake as normal. Then, once the muffins are cool, scoop out some (1-3 teaspoons) of the center from the top of the muffin, and pipe the cream cheese mixture into the muffin. Please note that this will make less muffins than the original method.

Substitutions & variations
Be sure to use pure pumpkin puree rather than pumpkin pie filling. Pumpkin pie filling already contains sugar and spices, so using it can make the muffins overly sweet and change the texture.
You can adjust the pumpkin pie spice to suit your taste. If you don't have pumpkin pie spice, use a combination of 3 tablespons ground cinnamon, 2 teaspoons ground ginger, 2 teaspoons ground nutmeg, 1 teaspoon allspice, and 1 teaspoon ground cloves. Measure from this mixture. Don't use all of it! Save the rest in a jar for later. You can also use cinnamon alone for a milder flavor.
For an extra bakery-style crunch, sprinkle the muffin tops with pepitas (shelled pumpkin seeds) before baking. Chopped pecans or walnuts would also be delicious if you prefer a nutty topping.

You can add chocolate chips to the pumpkin muffin batter for pumpkin chocolate chip cream cheese muffins. White chocolate chips are another good option and pair especially well with the cream cheese filling.
I recommend using full-fat block cream cheese for the filling. Reduced-fat cream cheese can be substituted, but the filling may be softer and less rich. Avoid whipped cream cheese because its extra air and moisture can change the texture of the filling.

Storing leftover pumpkin cream cheese muffins
These muffins taste best when freshly baked and cooled, but can be wrapped in plastic wrap or stored in an airtight container in the fridge for up to 3-4 days.
Check out more delicious Pumpkin recipes
- Pumpkin Flan
- Pumpkin Spice Pancakes
- No-Bake Pumpkin Pie
- Glazed Pumpkin Spice Donuts
- Pumpkin Pie Overnight Oats
- Pumpkin Pie Ice Cream - No Churn Recipe
























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