October 21st 2023

Pumpkin Cream Cheese Muffins filled with a tangy Cream Cheese filling and sweet chocolate chips! These moist Pumpkin muffins with a cheesecake middle are sure to impress, everyone loves this pumpkin muffin recipe even kids! It’s so easy to make and I make them into healthy pumpkin muffins by using whole wheat flour and better-for-you ingredients!

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We love moist Zucchini Muffins and Banana Bread! Fall is the perfect season for baking to use up all that canned pumpkin or pumpkin puree from winter squash. Make our Apple Spice Cake or Blueberry Muffins with a streusel topping for more fall baking ideas!

Pumpkin Muffins with Cream Cheese

Pumpkin cream cheese muffins is a sweetened pumpkin muffin recipe made like quick bread but moist as a cupcake. It’s like a moist pumpkin spice cake with a cheesecake filling sprinkled with chocolate chips! This is such an easy batter to whip up and the cream cheese filling has chocolate chips in it so you’re one step ahead.

Pumpkin muffins make the perfect individual-sized portions to bring to a Holiday gathering, potluck, or special occasion! You can line a muffin tin with decorative paper for an extra festive look (and omit greasing the muffin pans)! It’s the perfect dessert to use up any canned pumpkin this fall season but beware these pumpkin cheesecake muffins are very addictive!

Ingredients for Pumpkin Cream Cheese Muffins:

The main ingredient in pumpkin muffins is to use 100% pure canned pumpkin which is basically pumpkin puree with no added preservatives. Use a brand you love!

Pumpkin Muffins- come together quickly with baking staples of sugar, eggs, oil, salt, baking powder, cinnamon, baking soda, and flour. I like to use freshly ground soft white wheat but you can use all-purpose flour. I will include the adjustments in the recipe card.
Cheesecake Filling- is very simple and only includes a block of cream cheese, 1 egg (to set the cheesecake filling), chocolate chips, and sugar. Once you mix it together you put a heaping teaspoon of the mixture in the center of the muffin batter.

Baker’s tip: To fill the inside with the cheesecake filling, double the cream cheese mixture and layer the pumpkin batter and cheesecake filling together by dolloping part batter part cheesecake filling. Feel free to swirl the top with a toothpick for a marble design.

How To Make Pumpkin Muffins with Cream Cheese:

To make cream cheese pumpkin muffins you’ll need 2 muffin pans as this recipe makes 2 dozen muffins. I only use 2 mixing bowls, one for all the wet and dry ingredients and the other for the cheesecake filling as the topping. A hand mixer is all you need to whip these cream cheese pumpkin muffins up!

Preheat the oven to 350°F. Prepare the muffin pans: line 24 muffin cups with cupcake liners and set aside.
Make the pumpkin muffin batter by beating all of the ingredients together with an electric hand mixer. I like to beat the canned pumpkin, sugar, eggs, and oil first then I add in the dry ingredients and mix well.
Fill the cupcake liners 3/4 full with the pumpkin batter.
Beat together the cream cheese filling and fold in the chocolate chips. Put one heaping teaspoon of the cheesecake filling in the center of each muffin.
Bake pumpkin muffins for 20 minutes.

To Bake Mini Pumpkin Muffins: spray two mini muffin pans with cooking spray. Fill each tin 3/4 full and dollop a teaspoon full on top. Bake at 350°F for 10-15 minutes.

How To Store Pumpkin Muffins?

How long do pumpkin muffins last? Pumpkin cream cheese muffins are good for up to 3 days at room temperature because they have a small amount of cream cheese on top they don’t need to be refrigerated. They stay moist and soft for days at room temperature but if you are in a warm climate then keep them refrigerated to prevent bacterial growth. I like to use my airtight Tupperware container to store these pumpkin muffins and it makes traveling with them super easy!

Can You Freeze Pumpkin Cream Cheese Muffins?

How To Freeze Pumpkin Muffins- cool and wrap each muffin with plastic wrap. Place 6-9 muffins in a gallon freezer bag and freeze for up to 3 months. Thaw completely before serving.

Q&A

Can I make gluten-free Pumpkin Muffins?

This pumpkin cream cheese muffin recipe can be substituted with a gluten-free flour mix. Use about 345 grams or 2 3/4 cups of gluten-free flour.

Tips for the Best Pumpkin Muffins:

This recipe for pumpkin muffins was originally for 2 cups of white flour, if you’re into milliling your own flour I’ve converted this recipe to using whole grain! I feel great making whole-wheat pumpkin muffins for my family and the children love them!
Pumpkin chocolate chip muffins are best with semi-sweet or milk chocolate chips.
For a copycat to the Starbucks pumpkin cream cheese muffin, omit the chocolate chips and garnish the cheesecake filling with 1 tablespoon of toasted pumpkin seeds instead.
Make a hefty batch of this Pumpkin Muffins recipe for the freezer as an easy midday snack.
To make them healthy I like to use organic whole wheat flour, organic cane sugar, and non-GMO sunflower oil.

More Fall Baking Recipes:

More Winter Squash Recipes:

Have you tried these easy pumpkin muffins? Be sure to comment and leave a photo review down below for these pumpkin muffins with cream cheese!