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Fall is officially here, and that means it’s time to break out the pumpkin recipes! One of the best ways to embrace the flavors of the season is by indulging in a batch of homemade Pumpkin Cream Cheese Muffins. 

These delectable treats are a delightful fusion of tender pumpkin muffins and a rich swirl of cream cheese filling. 

stack of homemade pumpkin cream cheese muffins.
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If you love delicious pumpkin cream cheese muffins and baked goods with fall flavors, be sure to check out all of my pumpkin recipes!

Reasons to Make These Muffins

If you’ve ever enjoyed a Starbucks Pumpkin Cream Cheese Muffin, you’ll know exactly why this combination is so magical. 

The sweet cream cheese filling complements the moist pumpkin muffin perfectly. 

It’s like having dessert for breakfast!

  • Simple Ingredients: One of the best parts of this recipe is that it uses simple ingredients that you likely already have in your kitchen. From all-purpose flour to pumpkin puree, eggs to vanilla extract, everything comes together beautifully to create a harmonious flavor profile.
  • The Cream Cheese Filling: The star of the show in these muffins is undoubtedly the cream cheese filling. With each bite, enjoy a rich swirl of cream cheese running through the center of each muffin, giving them a delightful sweet taste.
  • A Taste of Autumn in Every BitePumpkin spice is the quintessential flavor of the fall season, and this recipe makes excellent use of it. The combination of the sweet cream cheese filling, tender pumpkin muffin, and pumpkin spice flavor creates a delightful symphony of flavors that’s perfect for a cozy fall breakfast or an afternoon treat with your favorite coffee.
  • The Copycat Starbucks Experience: For those who adore the Starbucks Pumpkin Cream Cheese Muffins, making these at home will give you the satisfaction of enjoying a copycat version. Plus, you can customize them to your liking, adding more or less cream cheese filling, a streusel topping, or even crunchy pumpkin seeds.
pumpkin cream cheese muffins on cooling rack.

Ingredients Needed

The ingredients used in this recipe are separated into two parts.

Pumpkin Muffin Ingredients

To make the pumpkin muffin portion, you will need all-purpose flour, pumpkin pie spice, baking powder, baking soda, salt, pumpkin puree, granulated sugar, brown sugar, eggs, vegetable oil, and vanilla extract.

ingredients needed to make pumpkin muffins

Cream Cheese Mixture Ingredients

You will need cream cheese, sugar, egg yolk and vanilla extract for the cheesecake topping that gets swirled into the muffin batter prior to baking.

ingredients needed to make cream cheese filling for pumpkin swirl muffins

How to Make Pumpkin Cheesecake Muffins

Prior to mixing the batter, you will need to preheat the oven and prepare your muffin pan by adding a muffin liner to each well or greasing them with nonstick spray or butter.

Make Pumpkin Muffin Batter

In a medium bowl, combine the dry ingredients. Whisk together the flour, pumpkin spice, baking powder, baking soda, and salt until well combined. Set it aside.

Next, you will combine the wet ingredients. Using a large bowl, mix together the pumpkin puree, sugar and brown sugar. 

Then, mix in the eggs, oil and vanilla extract.

Slowly whisk the flour mixture into the wet ingredients until there are no lumps. 

Mix the Cream Cheese Topping 

In a medium bowl with electric beaters, or in a stand mixer bowl with the whisk attachment, beat the softened cream cheese until smooth. 

Add in the sugar, egg yolk, and vanilla extract. Beat the mixture until it is fully combined.

Bake the Muffins

Fill the muffin cups evenly about 3/4 full with the pumpkin batter.

Top each muffin with a small spoonful of the delicious cream cheese filling.

Use a toothpick or a butter knife to swirl the cheesecake mixture into the pumpkin mixture.

Place the muffins into the preheated oven and bake for 20-22 minutes, or until a toothpick inserted in the center comes out clean. 

Once removed from the oven, allow the muffins to sit in the hot muffin tin for a few minutes before transferring them to a cooling rack.

Baking Tips

  • Use room temperature eggs and softened cream cheese.
  • If you use all of the pumpkin batter, the muffins may spill over. Reserve any excess to make an extra muffin.
  • Use a large cookie scoop for the pumpkin batter and a small cookie scoop for the cheesecake filling to make it easy and drip-free.
  • While they are baking, do not open the oven door to check on the muffins until they are nearing the end of their cooking time.
pumpkin cream cheese muffins.

FAQs

Can I use homemade pumpkin puree for this recipe?

Yes, homemade pumpkin puree works great, but canned pumpkin puree is also a convenient option.

How should I store leftover muffins?

Store them in an airtight container or wrap them in plastic wrap and store them in the refrigerator.

Can I freeze these muffins for later?

Yes, you can freeze them in an airtight container, in a resealable freezer bag, or wrapped in plastic wrap for up to three months.

Is it possible to make these muffins without the cream cheese filling?

Of course, you can make regular pumpkin muffins without the cream cheese filling for a simpler treat.

Can I substitute the pumpkin pie spice with individual spices?

Yes, you can use a combination of cinnamon, nutmeg, and cloves if you don’t have pumpkin pie spice.

Could you make extra large or mini versions of these muffins?

Absolutely, you can use mini muffin tins to make bite-sized Pumpkin Cream Cheese Muffins. Cooking time will need to be reduced. Likewise, jumbo muffin tins can be used but cooking time will need to be extended.

Can I use something other than vegetable oil in the muffin batter?

Yes, olive oil, melted butter, or melted coconut oil can all be used as a substitute for vegetable oil in this recipe. All will result in very moist pumpkin muffins.

Should I add chocolate chips to the muffin batter for extra flavor?

Yes, adding chocolate chips is a delicious twist to the traditional recipe if you’re a fan of chocolate and pumpkin.

bite taken out of homemade pumpkin cream cheese muffins.


Pumpkin Cream Cheese Muffins

Prep20 minutes
Cook20 minutes
Total40 minutes
Servings 12 muffins
Muffin or cupcake? Its hard to tell with these incredibly moist, super tasty, and slightly naughty Pumpkin Cheesecake Muffins. You will love them!

Ingredients 

muffin:

cheesecake topping:

Instructions 

  • Prep work: Preheat oven to 375°F. Place paper baking cups into muffin pan or spray muffin wells with cooking spray. Set aside.
  • Mix dry ingredients: In a medium bowl, whisk together flour, pumpkin spice, baking powder, baking soda, and salt until well combined. Set aside.
    mixing dry ingredients for pumpkin muffins
  • Mix wet ingredients: In large bowl, whisk together pumpkin, sugar and brown sugar. Mix in eggs, oil and vanilla extract.
    adding sugar and pumpkin to dry ingredients for pumpkin muffin recipe
  • Combine to make pumpkin batter: Slowly whisk the flour mixture into the wet ingredients until there are no lumps. Fill muffin cups evenly about 3/4 full. If you have excess batter, you may end up with enough for a 13th muffin to make a baker's dozen. If you use all of the batter, they may spill over. Tip: Using a large cookie scoop makes it easy and drip-free.
    pumpkin muffin batter
  • Make cream cheese topping: In a medium bowl with electric beaters, or in a stand mixer bowl with the whisk attachment, beat the cream cheese until smooth. Add in sugar, egg yolk, and vanilla extract and beat the mixture until it is fully combined.
    adding eggs to cream cheese filling.
  • Add topping: Top each muffin with a small spoonful (I use the small cookie scoop) of cream cheese mixture and use a toothpick to swirl it into the batter.
    cream cheese topping on pumpkin muffin batter.
  • Bake: Place muffins into the preheated oven and bake for 20-22 minutes, or until a toothpick inserted in the center comes out clean. Do not open the oven door to check on the muffins until they are nearing the end of their cooking time. Once removed from the oven, allow to sit in muffin tin for a few minutes before transferring to a cooling rack.
    baked pumpkin cream cheese muffins.

Notes

Store cooled leftover muffins in an airtight container in the refrigerator.

Nutrition

Calories: 263kcal, Carbohydrates: 43g, Protein: 5g, Fat: 8g, Saturated Fat: 4g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 2g, Trans Fat: 0.003g, Cholesterol: 65mg, Sodium: 266mg, Potassium: 187mg, Fiber: 2g, Sugar: 27g, Vitamin A: 5836IU, Vitamin C: 2mg, Calcium: 65mg, Iron: 2mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Did you make this? Leave me a comment below

This recipe was originally published in October 2017 and has been updated with helpful information, ingredient and process photos, as well as recipe tips. Don’t worry – the recipe hasn’t changed!

Hi! I’m Krissy.

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