These Pumpkin Cheesecake Muffins have all of the yummy flavors of fall, plus a sweet cream cheese swirl.  They are super moist, impossible to resist, require just a handful of ingredients, and can double as either breakfast or dessert.

If you love pumpkin, you can also try our Pumpkin Cupcakes, Pumpkin Muffins or Pumpkin Cream Cheese Danish.

A wire rack full of pumpkin cheesecake muffins.

Pumpkin Cheesecake Muffins

Once fall rolls around, these Pumpkin and cream cheese muffins with are one of the first recipes I like to make.  Not only are they absolutely delish, they are also incredibly easy to make.  In fact, the muffin batter only contains 4 ingredients: a box of spice cake mix, a couple of eggs, melted butter, and an entire can of pumpkin.

These cake mix pumpkin muffins are then swirled with a yummy cheesecake filling and baked to perfection.  They taste amazing with a big cup of coffee in the morning, as an afternoon snack with a glass of hot apple cider or even dessert with a scoop of vanilla ice cream.

Not a fan of cheesecake?  Try these Easy Pumpkin Muffins with brown sugar streusel instead. And if you’re looking for more pumpkin recipes, be sure to try our Pumpkin Fluff Dip, Pumpkin Cake with Cream Cheese Frosting, Pumpkin French Toast Bake, and Pumpkin Rice Pudding.

Baked pumpkin cheesecake muffins in a muffin pan.

Ingredients You Will Need

  • Pumpkin Puree: the easiest route to go is to buy unsweetened canned pumpkin puree.  You can also make your own Homemade Pumpkin Puree using small pie pumpkins or sugar pumpkins.
  • Eggs: any type of large eggs will work.
  • Butter: use unsalted butter for this recipe.  You can also substitute vegetable oil, or even half vegetable oil and half applesauce if you want something with a little less fat.
  • Cake Mix: try and find a Spice Cake Mix as it already has a great blend of pumpkin pie spices in it.  Both Betty Crocker and Duncan Hines have versions.
  • Cream Cheese: you want your cream cheese to be soft and at room temperature.  Either pull it from the fridge at least 1 hour in advance, or transfer to a microwave-safe container and heat for about 20-30 seconds at a time until softened.
  • Sugar: the cheesecake filling uses white granulated sugar.
  • Egg Yolk: you can reserve the white for another use, or throw it out.
  • Vanilla Extract: pure vanilla extract tastes best.
Three photos of cream cheese mixture being swirled into pumpkin muffin batter.

How to Make Pumpkin Cream Cheese Muffins

  1. Make the batter.  In a large mixing bowl, combine the pumpkin puree, eggs, and melted butter.  Whisk together until smooth. Add in spice cake mix. Mix until combined. 
  2. Scoop into muffin pans.  Grease or line 24 muffin tins with paper liners.  Using an ice cream scoop or a spoon, scoop the batter into the prepared muffin tins, filling them about 3/4 of the way full.
  3. Make the cheesecake topping.  In a small bowl, combine the room temperature cream cheese, egg yolk, sugar and vanilla and stir until smooth.  Add about 1 tablespoon of cream cheese mixture onto each muffin, then use a toothpick to swirl the cheesecake topping into the muffin mix.
  4. Bake.  Bake in a preheated 350 degree oven for 20-22 minutes, or until golden brown and a toothpick inserted into the center comes out clean. 
  5. Cool and serve.  Remove from the oven and let cool for a few minutes before removing the muffins from the muffin tin and cooling completely at room temperature.  Enjoy!
Pumpkin muffins cooling on a wire rack with one opened and cut in half.

Frequently Asked Questions

Can I freeze pumpkin muffins?

Yes!  These muffins freeze really well.  Just pop any extras into freezer bags and store in the freezer for up to 2 months.

How long will pumpkin cheesecake swirl muffins stay fresh?

As long as they are stored properly in an airtight container in the fridge, these muffins will stay fresh for up to 5 days.

How long do pumpkin cream cheese muffins take to bake?

That all depends on the size of your muffins and the temperature of your oven.  If you are using regular muffin tins and baking at 350 degrees, it should take between 20-22 minutes to bake. 

If you go with a mini size muffin pan, that time will decrease to only about 10-12 minutes.  Or, if you plan to bake these in loaf pans, you can expect it to take closer to 30-35 minutes.

Muffins cooling on a wire rack.

Recipe Variations

  • Pumpkin Swirl Cupcakes: treat these like cupcakes and top with cream cheese frosting.
  • Pumpkin Cheesecake Bread: bake this recipe in two 8”x4” loaf pans, swirling the cheesecake topping into each just before baking.  The bake time will increase, so keep an eye on it and check the doneness by inserting a toothpick into the center of the loaf.  If it comes out clean, your bread is baked.
  • Gluten-Free Pumpkin Muffins: try using a gluten-free spice cake mix to make your muffins gluten-free.  
  • Add-ins: try adding chopped pecans or walnuts, chocolate chips or even dried fruit to the pumpkin muffin batter before baking.
  • Mini Muffins: bake the batter in mini muffin pans for a baby shower, dessert buffet or snack for the kiddos.

Storing and Freezing Instructions

  • Refrigerator: store your leftover Pumpkin Muffins with Cheesecake Swirl in an airtight container in the fridge for up to 5 days.  We recommend bringing them to room temperature before eating.
  • Freezer: these freeze great for up to 2 months.  Store in an airtight container or freezer bags and thaw out in the fridge overnight or on the counter top for a few hours.
5 from 5 votes

Pumpkin Cheesecake Muffins Recipe

Author The Carefree Kitchen
These pumpkin cream cheese muffins have all of the yummy flavors of fall, plus a cheesecake swirl.  They are super moist, impossible to resist and can double as either breakfast or dessert.
Prep: 10 minutes
Cook: 25 minutes
Total: 35 minutes
Yields24 muffins

Ingredients

Pumpkin Muffins

  • 1 15-ounce can pumpkin puree
  • 2 large eggs
  • 1/2 cup butter, melted and cooled
  • 1 15.25-ounce box spice cake mix

Cheesecake Swirl Topping

  • 8 ounces cream cheese, room temperature
  • 1/4 cup sugar
  • 1 large egg yolk
  • 1 teaspoon vanilla extract

Instructions
 

  • Preheat oven to 350 degrees F. 
  • Grease or line 24 muffin tins with paper liners and set aside.
  • In a large mixing bowl, combine the pumpkin puree, eggs, and melted butter. Whisk together until smooth, then add the spice cake mix and mix until combined.
  • Using an ice cream scoop or a spoon, scoop the batter into the prepared muffin tins, filling them about 3/4 of the way full.
  • In a small bowl, combine the room temperature cream cheese, egg yolk, sugar, and vanilla and stir until smooth.
  • Add about 1 tablespoon of cheesecake topping onto each muffin, then use a toothpick to swirl the cheesecake topping into the muffin mix.
  • Bake for 20-22 minutes, or until golden brown and a toothpick inserted into the center comes out clean. 
  • Remove from the oven and let cool for a few minutes before removing the muffins from the muffin tin and cooling completely at room temperature. Enjoy!

Notes

Storing instructions: store muffins in an airtight container in the fridge for up to 5 days, or in the freezer for up to 2 months. 

Nutrition

Calories: 145kcal | Carbohydrates: 18g | Protein: 2g | Fat: 7g | Saturated Fat: 3g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 3g | Trans Fat: 1g | Cholesterol: 33mg | Sodium: 182mg | Potassium: 82mg | Fiber: 1g | Sugar: 12g | Vitamin A: 159IU | Vitamin C: 1mg | Calcium: 25mg | Iron: 1mg
Disclaimer: Nutritional values were calculated using a third-party tool and are provided as an estimation only.
Course Breakfast, Snack
Cuisine American
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More Of The Best Pumpkin Recipes

These Pumpkin Cream Cheese Swirl Muffins are super moist, impossible to resist and can double as either breakfast or dessert. They’re packed with the yummy flavors of fall with a sweet cream cheese swirl.

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5 from 5 votes (2 ratings without comment)

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3 Comments

  1. Have you tried folding the cream cheese mixture into the pumpkin mix before putting them in the muffin tin? It might just be me but I struggle with the swirling after it’s in the muffin liners.

  2. Cream cheese goes BEST with pumpkin at this time of year. These muffins were so yummy. The perfect grab and go breakfast!

  3. These muffins was really easy to make and I loved the texture so much

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