This easy recipe for pumpkin cream cheese muffins is guaranteed to make you pass on the pastry case at your local coffee shop. Whether you love a pretty swirl or a thick, cheesecake-style center, this recipe gives you both options for the ultimate fall treat.
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When Pumpkin Meets Cheesecake
If pumpkin bread and cheesecake had a muffin baby, this would be it. These pumpkin cream cheese muffins are moist, perfectly spiced, and swirled (or filled!) with tangy cheesecake goodness. They taste like fall and coffee-shop mornings, but better, because they’re made from scratch in your own kitchen.
Cream cheese, you complete me. You steal the show in cheesecake. You beautify brownies. You even managed to improve the best chocolate chip cookie recipe of all time. So it should come as no surprise that pumpkin + cream cheese = muffin perfection.
I’ve been making (and remaking) these muffins for years, testing every swirl, scoop, and dollop to find the perfect balance of creamy filling and fluffy pumpkin crumb. Whether you love a pretty swirl on top or a thick cheesecake center you can sink your fork into, this recipe gives you both options.
Grab your pumpkin pie spice and a can of pumpkin purée, and let’s make the ultimate fall muffin!
I’ve included quick notes below for a few key ingredients you’ll need to make these muffins. You can find the full list and measurements in the recipe card at the bottom of the post.
- Pumpkin purée: Use 100% pure canned pumpkin, not pumpkin pie filling, which already contains sugar and spices. You’ll only need 1 cup, so freeze the rest or make a batch of my favorite thick and fluffy pumpkin pancakes. If you prefer homemade purée, just make sure to drain off any excess liquid so your muffins bake up fluffy, not dense or gummy.
- Cream cheese: Use a full-fat block of cream cheese for the best taste and texture.
- Pumpkin pie spice: Store-bought works great, but my homemade pumpkin pie spice blend is well-tested and perfectly balanced.
- Butter: Unsalted butter gives this pumpkin cream cheese muffins recipe a rich flavor and denser crumb than those made with oil. Make sure it’s at room temperature so it creams smoothly with the sugar.
- Vanilla extract: Rounds out both the pumpkin batter and the cream cheese filling with warmth and depth.
Kelly’s Note from the Test Kitchen
I’ve made this recipe dozens of times since I first shared it back in 2015, sometimes piping the cheesecake mixture into the centers of the muffins, other times alternating scoops of the two batters and swirling them together.
Bottom line: There is no wrong way to marry pumpkin and cheesecake. Both ways deliver that cozy flavor combo that makes these a reader favorite year after year.
How to Make Pumpkin Cream Cheese Muffins (Two Ways!)
These are forgiving batters, so whether you pipe the cream cheese mixture into the center or swirl it in, you’re guaranteed something delicious. Here’s how to make both versions.
Option 1: Cream Cheese–Filled Muffins
If you’re after that thick, tangy cheesecake center, this is the method for you.
- Fill the cups: Spoon pumpkin batter into each muffin cup, filling about ¾ full.
- Add the filling: Transfer the cream cheese mixture to a piping bag (or a resealable plastic bag with the corner snipped off) and pipe about 1½ tablespoons into the center of each cup.
I recommend chilling the cheesecake filling for 10 to 15 minutes before piping. It firms up slightly, giving you better control and helping it maintain structure while baking.
Option 2: Swirled Pumpkin Cheesecake Muffins
If you love a marbled look, alternate scoops of pumpkin batter and cream cheese filling, then gently swirl them together with a toothpick or skewer.
Less is more when it comes to swirling—two to three gentle figure-eights are all you need for defined ribbons of cheesecake without overmixing.
Bake & Cool
Once you’ve filled your muffin cups with batter and filling, it’s time to bake. Bake at 350°F for 20 to 25 minutes, or until the tops spring back lightly. To check for doneness, insert a toothpick into the muffin just beside the cream cheese center. It should come out mostly clean, with a few moist crumbs attached. (Testing directly in the filling will always leave some residue, and that’s totally normal.)
Let the muffins cool in the pan for about 5 minutes, then transfer to a wire rack to cool completely.
These cream cheese pumpkin muffins taste even better once they’ve cooled — the pumpkin flavor deepens and the cheesecake centers firm up for the perfect texture and balance.
Success Tips & Variations
- Bring your ingredients to room temperature. Softened butter creams better with sugar, and room-temp eggs and cream cheese blend seamlessly into the batter. The result? A smooth, uniform crumb and a perfectly creamy center.
- Use muffin liners. I tested these with and without liners, and liners win every time. They keep the pumpkin muffins from sticking, help them rise evenly, and make cleanup (and sharing) a breeze.
- Don’t overfill. It’s tempting to pile the batter high, but leave a little room to rise. Filling each cup about ¾ full gives you beautifully domed tops without spillover.
- Make mini loaves. Try my Mini Pumpkin Cream Cheese Bread if you’re gifting or want a sliceable version.
- For a Starbucks-inspired finish, sprinkle pumpkin seeds (pepitas) on top before baking. They add a nice crunch and make your pumpkin cream cheese muffins look straight out of a bakery case.
Storage and Freezing Tips
- To store: Because these pumpkin muffins have a cream cheese filling, I recommend keeping them in an airtight container in the fridge. They’ll stay fresh for up to 5 days. Enjoy chilled or bring to room temperature before serving.
- To freeze: You can freeze these muffins, but note that the cheesecake centers may become slightly softer or a bit grainy once thawed. To minimize this, freeze them as soon as they’re completely cool. Arrange in a single layer on a baking sheet until firm, then transfer to a freezer-safe bag or container with parchment between layers. Freeze for up to 2 months. Thaw overnight in the fridge, then warm gently in a 300ºF oven for a few minutes to bring back that fresh-baked feel.
Kelly’s Tip: If you know you’ll be freezing them, skip paper liners as they tend to pull away after thawing. Instead, generously grease your muffin tin with cooking spray.
Ingredients
For the muffins:
- 1 2/3 cups all-purpose flour
- 1/2 teaspoon baking powder
- 1 teaspoon baking soda
- 1/2 teaspoon salt
- 2 1/2 teaspoons pumpkin pie spice
- 1/2 cup unsalted butter, at room temperature
- 1 1/3 cups sugar
- 1/2 teaspoon vanilla extract
- 2 large eggs
- 1 cup canned pumpkin
- 1/3 cup water
For the cream cheese filling:
- 1 (8-oz.) package cream cheese, at room temperature
- 2 Tablespoons sugar
- 1 large egg
- 1 teaspoon vanilla extract
Instructions
Make the muffins:
- Preheat the oven to 350ºF. Line a muffin pan with baking cups.
- In a large bowl, sift together the flour, baking powder, baking soda, salt and pumpkin pie spice. Set the bowl aside.
- In the bowl of a stand mixer fitted with the paddle attachment, cream together the butter, sugar and vanilla until light and fluffy, about 2 minutes. Add the eggs, one at a time, then add the pumpkin and mix until combined.
- Alternately add the dry ingredients and water to the bowl, beginning and ending with the dry ingredients. Blend the batter well, scraping down the sides as needed. Set the batter aside.
Make the cream cheese filling:
- In the bowl of a stand mixer fitted with the paddle attachment, beat together the cream cheese, sugar, egg and vanilla.
- Alternately add dollops of the pumpkin batter and cream cheese filling into the muffin cups, filling each ¾ full. Using a toothpick or sharp knife, swirl together the mixture.
- Bake the muffins for 20 to 25 minutes or until a toothpick inserted comes out clean. Allow the muffins to cool in the pan for 5 minutes then transfer them to a rack to cool completely.
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How to Make Pumpkin Cream Cheese Muffins (Better Than Starbucks!) #pumpkinmuffins #pumpkinrecipe
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Kelly’s Notes
- To make cream cheese–filled pumpkin muffins: Spoon pumpkin batter into each muffin cup, filling about ¾ full. Chill the cream cheese mixture for 10–15 minutes so it firms up slightly, then transfer it to a piping bag (or zip-top bag). Snip the tip and pipe about 1½ tablespoons into the center of each cup. Bake as directed.
- To store: Let muffins cool completely, then store in an airtight container in the fridge for up to 5 days. For the best texture, bring them to room temperature before serving.
- To freeze: Once completely cool, arrange muffins in a single layer on a baking sheet until firm, then layer between parchment in a freezer-safe container. Freeze for up to 2 months. Thaw overnight in the fridge. The cheesecake centers may lose a bit of their creamy texture once thawed, but the flavor stays just as delicious.
- ★ Did you make this recipe? Don’t forget to give it a star rating below!
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I used to love the Starbucks muffins, but I hate paying the price these days, so I thought I’d try this recipe (I piped the filling into the center rather than swirling it). They turned out so moist and flavorful. The cream cheese center is just sweet enough. I’ll be making a second batch to bring to work!
Love this, Margie!
Yum
Does this recipe work at High Altitude: Denver, Co?
Chocolate Chip Cookie Recipe WORKS WONDERFUL! THANK YOU!!
So glad you’re enjoying the High-Alt CCC’s recipe! I have not tried this specific recipe at high altitude so I can’t say with certainty what the results would be.
If we don’t have a stand mixer, would a hand mixer work as well?
And for that nutrition info, what is the serving size; is it for one muffin?
Absolutely, Alex! You can make this recipe without a stand mixer. Enjoy!
Just made the pumpkin muffins. They are great. Eating one right now from the oven. Love them.
So glad you enjoyed the recipe, Deborah!
I made these, but low cholesterol. Egg beaters for eggs, margerine for butter, neufchatel cream cheese. 2 mg cholesterol per muffin vs 46mg. They came out fine!
Awesome! I’m so glad you enjoyed the recipe, Betty!
If I want to use real pumpkin and not canned what do you suggest?
Hi Krystie! I’ve never tried this recipe using fresh/roasted pumpkin, but I think you’d want to really drain out any excess moisture. Let me know if you give it a shot!
Hi Kelly, as it’s hard to get cans of pumpkin puree here in Germany, do you think pumpkin puree from the baby food section would work the same? Thanks! Katja
That just might work, Katja! Let me know if you give it a shot!
… tried it today with baby food (pure pumpkin) and it worked very well. ;)
Woohoo! I’m so glad it worked out, Katja!
So beautiful and delicious! Thank you!
You’re so welcome, Cindy! I’m thrilled you enjoyed the recipe!
These are delicious and easy to make. My grandson loves them for breakfast.
I’m so thrilled to read this, Lucille!
I made the recipe as written but replaced the wheat flour with King Arthur gluten free flour. Butter was my shortening. I used whole milk in place of the water. Part way through the baking, my oven failed. I cooked these in a slow oven for a very long time, then finished them with the broiler. They came out perfect – not dry and not doughy. I will definitely make again!
Wow! I’m so glad you enjoyed the recipe, Diane!
would love this in chocolate muffins…..would it work the same?
Sure!