These pumpkin cream cheese muffins are super soft pumpkin muffins filled with cream cheese. These pumpkin muffins are full of spices and bake really tall. They taste amazing and the cream cheese filling makes a satisfying treat in the middle!

Close up of pumpkin cream cheese muffins.

These pumpkin cream cheese muffins are a delicious fall breakfast with lots of pumpkin spice flavor combined with a sweet cream cheese filling. They are the BEST pumpkin muffins and anyone who loves pumpkin spice flavor will love them. The best part is that it is an easy recipe with simple ingredients and only 8 steps! Make this pumpkin muffin recipe your go to breakfast this pumpkin season!

For more pumpkin recipes, try Pumpkin Cupcakes, Caramel Pumpkin Cheesecake Bars, and Pumpkin Cinnamon Rolls.

Try pumpkin chocolate chip cookies.

Why This Pumpkin Cream Cheese Muffin Recipe Works

  • Pumpkin flavor- These muffins welcome fall with pumpkin flavor and have lots of pumpkin spices! The perfect fall treat!
  • Cream cheese filling- Pumpkin and cream cheese are a perfect combination, and this cheesecake filling feels like a surprise treat in the middle!
  • Soft muffins- These muffins are tall and fluffy! They are moist muffins with the perfect tender muffin texture that makes it hard to stop eating them!
Stack of two muffins.

Ingredient Notes

Here are some notes on the ingredients. For a full ingredients list, check out the recipe card below.

  • Pumpkin puree- Make sure not to use a pumpkin pie filling as it has added ingredients we do not want. You can use canned pumpkin puree or homemade pumpkin puree.
  • Sour cream- Use full fat sour cream or greek yogurt. Pull this out 2 hours before baking.
  • Egg- Pull the large egg out 2 hours before using.
  • Baking powder + Baking soda- Both are used to give the muffins a better rise.
  • Unsalted butter- The butter needs to be melted and then cooled before use. If it is too warm it will affect the texture.
  • Brown sugar- I used light brown sugar, but dark brown sugar will work too.
  • Buttermilk- Pull this out 2 hours before baking. You can substitute in milk if you do not have buttermilk.
  • Cream cheese- Pull this out 2 hours before baking to get to room temperature.
  • Coarse sugar- A coarse sugar will make a better crunchy sugar topping on top of the muffin, but regular can be substituted if needed. I use Sugar In The Raw.

Step By Step Instructions- Pumpkin Muffin Batter and Cream Cheese Filling

Here is how to make and bake these pumpkin cream cheese muffins.

STEP 1: Dry ingredients. Use a large bowl to mix together the all purpose flour, baking powder, baking soda, salt, cinnamon, pumpkin pie spice, and nutmeg. Set it aside. Prep the pumpkin puree now by placing it on a plate and pressing a paper towel into it to absorb excess liquid. Do this roughly 4 times.

STEP 2: Wet ingredients. In a separate bowl, mix the melted butter, pumpkin puree, brown sugar, egg, vanilla extract, sour cream, and buttermilk. Pour them into the flour mixture and mix them until combined.

Wet ingredients in a glass bowl.
Muffin batter in a glass bowl.

STEP 3: Prep. Preheat the oven to 425ยฐF. Meanwhile, line a 12 cup muffin tin with 6 muffin liners alternating holes. The extra space allows for a higher rise.

STEP 4: Scoop. Use a large cookie scoop (2 TBSP or 2 oz) to scoop a heaping scoop of pumpkin muffin batter into each liner. Sprinkle the coarse sugar on top.

STEP 5: Beat cream cheese filling. Use a small bowl and hand mixer to beat cream cheese, sugar, flour, milk, and vanilla extract on high speed until smooth.

Cream cheese filling in a glass bowl.

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STEP 6: Pipe filling. Place the cream cheese mixture in a piping bag. Press the tip of the bag into the center of each muffin and squeeze until a dollop appears in the center. Use all of the filling between the 12 muffins (2 muffin tins)

Muffin batter in a cupcake tin.
Cream cheese in the muffin batter.

STEP 7: Bake. Bake at 425ยฐF for 6 minutes, then reduce the temperature to 350ยฐF and bake for 6-8 minutes. They are done when a toothpick inserted into the muffin comes out clean. Avoid the filling for this test.

STEP 8: Cool. Let the muffins cool in the hot pan for 10 minutes before transferring them to a cooling rack to cool completely.

Expert Baking Tips

  • Flour- Make sure the flour is spooned and leveled. If you stick the measuring cup into the flour, it will compact it. Compacted flour will dry out the muffins.
  • Bake 6 muffins at a time, to get a bigger rise and larger dome. A bigger rise also gives them a better texture.
  • It is easy to over mix muffin batter. As soon as it is combined, stop mixing.
  • Muffins are baked at a high heat first to activate the rising agents and get a taller muffin.
  • For the toothpick test try to get the toothpick close to the center of the muffin without going into the filling. We want to test if the muffin batter is fully baked, but the cream cheese will stick to the toothpick.
Top view of pumpkin cream cheese muffins on a wire rack.

FAQ

What is the secret to fluffy muffins?

Make sure that the dairy ingredients are at room temperature before using. Also, the sour cream will help the muffins be very fluffy.

Why are my muffins dry?

Dry muffins have to do with over baking or over measuring too much flour. If your oven runs hot, check the muffins early.

Can I use a mini muffin pan?

Yes you can! You will have to reduce your bake time for mini muffins compared to regular size muffins.

Why do you only put 6 muffins in your 12 muffin pan?

Separating the muffins only using alternating muffin cups allows the air to get to the muffins evenly. This will also allow them to bake faster than a full 12 muffins. This extra room will give your muffins a larger rise and incorporate more air for an better texture.

Storing and Freezing

Store these pumpkin cream cheese muffins in the fridge in an airtight container. Store up to 5 days.

Freezing

The pumpkin cream cheese muffins can be frozen. Wrap in plastic wrap and store in an airtight container and freeze up to 30 days.

Thaw frozen muffin for 1-2 hours before eating.

Top view of muffin.

Other Muffin Recipes To Try

Make sure to leave a STAR REVIEW if you loved this recipe! Make sure to tag me on Instagram @stephaniesweettreats. To get more ideas follow me on Pinterest.

Close up of pumpkin cream cheese muffins.
5 from 13 reviews

Pumpkin Cream Cheese Muffins

These pumpkin cream cheese muffins are super soft pumpkin muffins filled with cream cheese. These pumpkin muffins are full of spices and bake really tall.
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Ingredients
 
 

Pumpkin Muffins

  • 2 cups All-purpose flour
  • 2 tsp Baking powder
  • 1/2 tsp Baking soda
  • 1/2 tsp Salt
  • 2 tsp Ground cinnamon
  • 1 tsp Pumpkin pie spice
  • 1/4 tsp Ground nutmeg
  • 15 oz Pumpkin puree, 1 can of puree
  • 1/2 cup Unsalted butter, melted and cooled
  • 3/4 cup Brown sugar, packed light or dark
  • 1 Large egg, room temperature
  • 1 tsp Pure vanilla extract
  • 1/4 cup Sour cream, room temperature
  • 1/2 cup Buttermilk, room temperature
  • Coarse sugar, like sugar in the raw

Cream Cheese Filling

  • 4 oz Cream cheese, room temperature
  • 2 TBSP White granulated sugar
  • 1 tsp All-purpose flour
  • 1 tsp Milk
  • 1 tsp Pure vanilla extract

Instructions
 

Pumpkin Muffins

  • In a large bowl, mix the flour, baking powder, baking soda, salt, cinnamon, pumpkin pie spice, and nutmeg. Set aside. Place the pumpkin puree on a plate. Press a paper towel on the plate. Do this about 4 times so it soaks up the extra moisture.
    2 cups All-purpose flour, 2 tsp Baking powder, 1/2 tsp Baking soda, 1/2 tsp Salt, 2 tsp Ground cinnamon, 1 tsp Pumpkin pie spice, 1/4 tsp Ground nutmeg, 15 oz Pumpkin puree
  • In a separate bowl, mix the melted butter, pumpkin puree, brown sugar, egg, vanilla, sour cream, and buttermilk. Pour the wet ingredients into the dry. Mix until just combined.
    1/2 cup Unsalted butter, 3/4 cup Brown sugar, 1 Large egg, 1 tsp Pure vanilla extract, 1/2 cup Buttermilk, 1/4 cup Sour cream

Cream Cheese Filling

  • Preheat the oven to 425โ„‰. Place 6 muffin liners per 12 cup muffin pan (separate them out, this gives them a chance to rise higher)
  • Use a large cookie scoop and scoop a heaping scoop into each liner. Sprinkle the coarse sugar on top.
    Coarse sugar
  • In a small bowl using a hand mixer, beat the cream cheese, sugar, flour, milk, and vanilla on high speed until smooth.
    4 oz Cream cheese, 2 TBSP White granulated sugar, 1 tsp All-purpose flour, 1 tsp Milk, 1 tsp Pure vanilla extract
  • Place the cream cheese filling in a piping bag. Place the bag in the middle of muffin batter. Squeeze until a dollop appears in the center of the muffin. You will use all of the filling for the 12 muffins.
  • Bake at 425โ„‰ for 8 minutes. Then, turn the oven down to 350โ„‰. Bake for another 6-8 minutes. Bake until a toothpick inserted comes out clean.
  • Let the muffins sit in the hot pan for 10 minutes before transferring to a cooling rack. Cool completely before storing in the fridge. These taste best cold.

Notes

Flour- Make sure flour is spooned and leveled or use a kitchen scale. Compacted flour can dry out the muffins.
High altitude baking- Add an extra 2 TBSP of flour.
Pull out dairy ingredients 2 hours before baking.
Calories: 269kcal, Carbohydrates: 36g, Protein: 4g, Fat: 13g, Saturated Fat: 8g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 3g, Trans Fat: 0.3g, Cholesterol: 34mg, Sodium: 262mg, Potassium: 152mg, Fiber: 2g, Sugar: 18g, Vitamin A: 5927IU, Vitamin C: 2mg, Calcium: 96mg, Iron: 2mg
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