Pumpkin Cheesecake Swirl Cupcakes

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These Pumpkin Cheesecake Cupcakes are a fun combination of pumpkin cake and pumpkin cheesecake, all in one easy-to-eat cupcake! They are super moist and totally addicting!

Looking for more pumpkin dessert recipes? Don’t miss out on this easy pumpkin cake or these festive pumpkin cupcakes!

This post is sponsored by Challenge Dairy, but all opinions are my own.

Pumpkin Cheesecake Swirl Cupcakes Recipe

So lately I’ve been hooked on a new show. Summers are always kind of brutal for TV, so I turn to Netflix and such to get me through. One show that I know so many people love that I never even tried to watch was Grey’s Anatomy. I’m not sure why, it just had never appealed to me.

Well, summer tv got bad enough towards the end that I finally caved. I figured it’d be good to get me through to the start of the new seasons of everything. Now the joke’s on me because I’m totally hooked! All my shows are coming back on and I’m totally uninterested because I’m in love with Meredith and Derek. I’m now in season 8 and the only show I’m really willing to take a break from it for for is Outlander. The binging is real and totally a problem.

Pumpkin Cheesecake Swirl Cupcakes with pumpkin candies on top.

Speaking of binging, these cupcakes are totally bing-worthy as well. Not only is pumpkin one of the best parts of fall, they combine both cake and cheesecake into one – with such little effort! How could you resist? Why would you want to?!

Pumpkin Cheesecake Swirl Cupcakes showing layers.

How to Make Pumpkin Cheesecake Cupcakes

These cupcakes start with the cupcake and cheesecake base. The cheesecake mixture and cake mixture are both made separately and then layered into the cupcake liners. Because I’m a fan of more layers, there’s three layers of cake and two layers of cheesecake in each one. Ultimately you end up with a nice amount of cheesecake swirled through the cupcakes so every bite ensures you get both.

Of course these cupcakes use both Challenge Butter and Cream Cheese. They are both such great quality dairy products. The butter is 100% real cream and farm to fridge in two days. It really is so creamy! I always love that when I soften it to room temperature to bake with, I can really tell just how creamy it is and it stays that way, unlike other brands.

Pumpkin Cheesecake Swirl Cupcakes on a plate.

The Challenge Cream Cheese was also used in the classic cream cheese frosting on top. It’s as close to homemade as it gets with nothing artificial and no added hormones. I’m a big fan! The frosting itself is a simple classic with a touch of cinnamon to compliment the spices in the cupcake. I love the addition of it to the cupcakes! I used a little less frosting per cupcake than I normally do just because there’s so much awesomeness in the cupcake, I didn’t want the frosting to over power it.

The final cupcakes scream fall and are a such a great way to get your fix of two things – cake and cheesecake – all at once! They are fairly easy to put together and a great treat for sharing for the holidays! I hope you enjoy them as much as we did!

Close up of pumpkin cupcakes.


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close up image of Pumpkin Cheesecake Swirl Cupcake

Pumpkin Cheesecake Swirl Cupcakes

  • Author: Lindsay
  • Prep Time: 40 minutes
  • Cook Time: 17 minutes
  • Total Time: 57 minutes
  • Yield: 14-16
  • Category: Dessert
  • Method: Oven
  • Cuisine: American


These Pumpkin Cheesecake Swirl Cupcakes are a combination of moist pumpkin cake and creamy pumpkin cheesecake. Perfect for a fun and festive fall dessert!


Cheesecake Filling

  • 6 ounces (170gChallenge Cream Cheese, room temperature
  • 1/4 cup (52g) sugar
  • 3 tablespoons (43g) sour cream
  • 3/4 teaspoon vanilla extract
  • 1 large egg white, room temperature

Pumpkin Cupcakes

  • 1/4 cup (56gChallenge Unsalted Butter, melted and slightly cooled
  • 1/4 cup (60ml) vegetable oil
  • 5 tablespoons (75ml) milk, room temperature
  • 1 cup (108g) light brown sugar, unpacked
  • 1 teaspoon vanilla extract
  • 2 eggs
  • 1 1/4 cup + 2 tablespoons (179g) all purpose flour
  • 1 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1 teaspoon ground cinnamon
  • 1/4 teaspoon ground nutmeg
  • 1/4 teaspoon ground ginger
  • 1/4 teaspoon ground cloves
  • 1/4 teaspoon salt
  • 1 cup (233g) canned pumpkin puree

Cream Cheese Frosting


1. Preheat the oven to 350 degrees and line a cupcake pan with cupcake liners.
2. To make the cheesecake filling, add the cream cheese and sugar to a large mixer bowl and beat until smooth.
3. Add the sour cream and vanilla extract and beat until well combined.
4. Add the egg white and beat until well combined. Set mixture aside.
5. To make the cupcake batter, add the butter, oil and milk to another large mixer bowl and whisk until smooth.
6. Add the brown sugar and whisk until well combined.
7. Add the vanilla extract and eggs and whisk until well combined.
8. In a separate medium-sized bowl, combine the flour, baking powder, baking soda, cinnamon, nutmeg, ginger, cloves and salt.
9. Add the dry ingredients to the wet ingredients and beat until well combined.
10. Fold in the pumpkin puree until well combined.
11. Add 1 tablespoon of cupcake batter to the bottom of each cupcake liner, spreading it so that it covers the bottom.
12. Add 1/2 a tablespoon of the cheesecake filling to the center of the batter.
13. Add another tablespoon of cupcake batter and another half tablespoon of cheesecake batter.
14. Top the cupcakes with another tablespoon of cupcake batter, then swirl everything around with a toothpick.
15. Bake the cupcakes for 15-17 minutes, or until a toothpick inserted in the middle comes out with a few crumbs.
16. Remove cupcakes from the oven and allow to cool for 2-3 minutes, then remove to a cooling rack to finish cooling. The centers may fall a bit as they cool, which is ok. It’s from the cooling of the cheesecake layers.
17. To make the frosting, beat the cream cheese and butter together in a large mixer bowl until well combined and smooth.
18. Add the powdered sugar and mix until well combined and smooth.
19. Add the cinnamon and vanilla extract and mix until well combined.
20. Pipe the frosting onto the cooled cupcakes. I used Ateco tip 844.
21. Refrigerate the cupcakes until ready to serve. Cupcakes are best when stored well covered in the fridge for 3-4 days.


  • Serving Size: 1 Cupcake
  • Calories: 267
  • Sugar: 26 g
  • Sodium: 171.5 mg
  • Fat: 11.8 g
  • Carbohydrates: 36.9 g
  • Protein: 4.5 g
  • Cholesterol: 45.8 mg


Pumpkin Cheesecake Cupcakes Pinterest image.

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  1. Tatianna

    This recipe was a HIT! The entire family loved it! I made 2.5 batches and gave the extras to friends. Even my pumpkin hater friends loved these cupcakes. Planning on making more for Christmas potluck absolutely must try this recipe you will not regret it. My biggest tip is clean as you go and you will be left with ZERO mess at the end besides the cupcake pan. The recipe was broken down so perfectly thank you!

  2. Katherine

    This was a delicious cupcake! I added an extra egg by accident but still was lovely texture. I used extra large cupcake holders and it made a nice serving. Will definitely be making this again. I’ve tried other recipes and for me this one outshined them all.

  3. Alecia

    These cupcakes were so delicious! I brought them to our Thanksgiving dinner and everyone raved about them. Thank you for a great recipe!

  4. Dakota

    Hi, I would like to make these cupcakes for my friend tomorrow but don’t have Challenge butter. Do you have to use the Challenge butter and cream cheese or could you use a different brand?

  5. Dortha

    Hi, I would like to make these amazing looking cupcakes for my friend today but don’t have Challenge butter. Do you have to use the Challenge butter and cream cheese or could you use a different brand?

  6. Lauralyn

    I’ve made these cupcakes several times, and they are delicious! Would it be possible to make them as a 9″x13″ cake, do you think?

    1. Lindsay

      It’s very hard for me to say without being there. It could be that they needed to bake a little longer, or something else.

  7. Alisha

    I just made these. They are divine. I wanted something like Libby’s pumpkin roll, but in smaller portions, and prettier. I doubled the recipe and made mini cupcakes, for a party. Other than that, followed recipe exactly. Very pumpkiny, just the right amount and balance of spices, The cupcake was moist and light. The cheesecake swirls cooked up nicely, and there were a lot of them. With the frosting it was very cream cheesy, which i wanted. i also liked the butter to cream cheese ratio in the frosting. The minis tasted like you put a pumpkin cheesecake in your mouth. Thank you for this fantastic recipe! I’ll definitely be making it every year.

  8. OJ

    These look SOO good!!!!! Thanks Lindsay! Oh, and we got your cake book in the mail yesterday! It is beautiful!! Great job! Can’t wait to start baking! 

  9. Michele

    I LOVE your blog! These cupcakes look amazing! What can be better than cheesecake and pumpkin?? I’m also in love with Outlander! Just caught up this morning. Have you read the books? I’m on An Echo In the Bone.

    1. Lindsay

      Thanks so much Michelle! I haven’t read the books. My mom and several friends have, but I’ve held off. Once I read the books for something, the movie/tv show is never quite the same. I’m afraid for the books to ruin the show for me. 🙂

  10. Kimberly Davis

    These look amazing! I’ve been trying to find a good cupcake recipe to make for Halloween, and I think these might be the ones!

About Lindsay

I'm a wife and a mom to twin boys and a baby girl! And I've got a serious sweets addiction! Bring on the treats!

Scripture I’m Loving

“Come to me, all you who are weary and burdened, and I will give you rest. Take my yoke upon you and learn from me, for I am gentle and humble in heart, and you will find rest for your souls.” Matthew 11:28-29