Moist Pumpkin Cream Cheese Muffins

Finding the perfect fall baking recipe that satisfies everyone’s sweet tooth while still feeling somewhat wholesome can be tricky. Between trying to use up that leftover pumpkin puree from Halloween and wanting something that works for both breakfast and dessert, it’s easy to get stuck in a baking rut.

Thankfully, these pumpkin cream cheese muffins hit the sweet spot: they’re packed with cozy fall flavors, have just the right amount of indulgence from the cream cheese, and are simple enough to whip up on a weekend morning when the whole family is craving something special.

What Kind of Pumpkin Puree Should I Use?

For these muffins, you’ll want to use plain pumpkin puree, not pumpkin pie filling – there’s a big difference! Pumpkin puree is just cooked and mashed pumpkin with no added spices or sugar, while pumpkin pie filling already has spices and sweeteners mixed in. You can find canned pumpkin puree in the baking aisle of most grocery stores, and brands like Libby’s work perfectly. If you’re feeling ambitious, you can also make your own by roasting a sugar pumpkin and pureeing the flesh, but honestly, the canned stuff is convenient and gives consistent results every time.

Options for Substitutions

This recipe is pretty forgiving when it comes to swaps, so here are some options if you need to make changes:

• Oil: You can replace the oil with melted butter (use the same amount) for a richer flavor, or try applesauce for a lighter version – though the texture will be slightly denser.
• Pumpkin puree: Make sure you’re using pure pumpkin puree, not pumpkin pie filling. If you’re out, you can substitute with sweet potato puree or butternut squash puree in the same amount.
• Milk: Any milk works here – whole, 2%, almond, or oat milk. Buttermilk will add a nice tang, but reduce the baking soda to ¾ teaspoon if you use it.
• Pumpkin pie spice: Don’t have pumpkin pie spice? Mix together 2 teaspoons cinnamon, 1 teaspoon ground ginger, ½ teaspoon nutmeg, and ½ teaspoon allspice.
• Cream cheese: The cream cheese filling is really what makes these special, so I wouldn’t skip it. Make sure it’s at room temperature for easy mixing – cold cream cheese will create lumps.
• All-purpose flour: You can substitute with a 1:1 gluten-free flour blend if needed, though the texture may be slightly different.

Watch Out for These Mistakes While Baking

The biggest mistake when making pumpkin cream cheese muffins is overmixing the batter, which leads to tough, dense muffins instead of light and fluffy ones – mix just until the ingredients are combined and you still see a few streaks of flour.

Another common error is using pumpkin pie filling instead of pure pumpkin puree, which contains added spices and sugar that will throw off your recipe’s balance.

Make sure your cream cheese is at room temperature before making the filling, as cold cream cheese will create lumps that won’t smooth out, and don’t overfill your muffin cups – aim for about ¾ full to prevent overflow.

Finally, resist the urge to open the oven door during the first 15 minutes of baking, as this temperature drop can cause your muffins to sink and become heavy.

What to Serve With Pumpkin Cream Cheese Muffins?

These muffins are perfect on their own for breakfast or an afternoon snack, but they pair beautifully with a hot cup of coffee or spiced chai tea. I love serving them alongside scrambled eggs and crispy bacon for a cozy fall brunch that feels extra special. They’re also great with a dollop of whipped butter or even a drizzle of maple syrup if you want to make them feel more like dessert. For a lighter option, try them with Greek yogurt and a sprinkle of granola, or just enjoy them warm from the oven with nothing but a steaming mug of your favorite morning drink.

Storage Instructions

Keep Fresh: These pumpkin cream cheese muffins taste amazing for days! Store them in an airtight container at room temperature for up to 3 days, or in the fridge for up to a week. The cream cheese filling means they’re best kept cool, especially if your kitchen gets warm.

Freeze: I love freezing a batch of these muffins for busy mornings. Wrap each muffin individually in plastic wrap or store them in a freezer-safe container for up to 3 months. They thaw perfectly and still taste fresh!

Warm Up: To enjoy your muffins warm, just pop them in the microwave for 15-20 seconds if they’re at room temperature, or 30-45 seconds if frozen. You can also warm them in a 300°F oven for about 5 minutes to get that fresh-baked feel again.

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 2500-2750
• Protein: 34-40 g
• Fat: 115-130 g
• Carbohydrates: 330-360 g

Ingredients

For the pumpkin muffin batter:

• 1/2 cup canola or vegetable oil
• 1 cup white sugar
• 1 tsp pure vanilla extract
• 1 1/4 cups canned pumpkin puree
• 2 large eggs
• 1/2 cup milk
• 1 3/4 cups all-purpose flour
• 1 tsp baking soda
• 1/2 tsp baking powder
• 1/2 tsp table salt
• 4 tsp ground pumpkin pie spice

For the cream cheese swirl:

• 8 oz cream cheese block
• 1/4 cup granulated sugar
• 1 large egg
• 1 tsp vanilla flavoring

Step 1: Preheat the Oven and Prepare Muffin Tins

Preheat your oven to 375 degrees Fahrenheit to ensure it reaches the right temperature for baking.

Meanwhile, line your muffin pans with paper cups so they’re ready for the batter.

Step 2: Mix the Wet Ingredients for Muffins

• 1/2 cup canola or vegetable oil
• 1 cup white sugar
• 1 tsp pure vanilla extract
• 1 1/4 cups canned pumpkin puree
• 2 large eggs
• 1/2 cup milk

In a large bowl, whisk together the canola or vegetable oil, white sugar, and pure vanilla extract until fully incorporated.

Add the canned pumpkin puree, eggs, and milk.

Whisk until the mixture is smooth and well combined.

Step 3: Combine Dry Ingredients and Finish Muffin Batter

• 1 3/4 cups all-purpose flour
• 1 tsp baking soda
• 1/2 tsp baking powder
• 1/2 tsp table salt
• 4 tsp ground pumpkin pie spice

In a separate bowl, mix the all-purpose flour, baking soda, baking powder, table salt, and ground pumpkin pie spice.

Gradually add this dry mixture to the wet ingredients, whisking until just combined.

Be careful not to overmix, which can make the muffins dense—I always stop mixing as soon as no dry spots remain.

Step 4: Make the Cream Cheese Filling

• 8 oz cream cheese block
• 1/4 cup granulated sugar
• 1 large egg
• 1 tsp vanilla flavoring

In a separate large bowl, beat the cream cheese block and granulated sugar together using an electric mixer until smooth and creamy.

Add in the egg and vanilla flavoring, and continue mixing—scraping down the sides of the bowl as needed—until the filling is uniform.

Set aside until ready to use.

Step 5: Assemble Muffins and Swirl Batters

• pumpkin muffin batter (from Steps 2 & 3)
• cream cheese filling (from Step 4)

Using a #24 scoop or by filling muffin cups about 2/3 full, scoop the pumpkin muffin batter into the prepared muffin cups.

Top each with a spoonful of the cream cheese filling (about a #50 scoop or a bit more than 1 tablespoon per muffin).

Using a butter knife, gently fold (not swirl) the two batters together: insert the knife through the center of the muffin batter and scrape along the bottom, then draw the knife out at the edge and fold the batter back toward the center.

Repeat 2 to 3 times to create a marbled effect; less mixing gives the best look.

Step 6: Bake and Cool the Muffins

Bake the assembled muffins in the preheated oven at 375˚F for 15-18 minutes, or until a toothpick inserted in the center comes out with a few moist crumbs.

Avoid over-baking to keep the muffins moist.

Once baked, let the muffins cool completely before serving.

I like to let them cool in the pan for a few minutes, then transfer them to a wire rack for best texture.

Moist Pumpkin Cream Cheese Muffins

Delicious Moist Pumpkin Cream Cheese Muffins recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 11 minutes mins

Cook Time 23 minutes mins

Total Time 34 minutes mins

Servings 4

Calories 2625 kcal

Ingredients

  

For the pumpkin muffin batter:

• 1/2 cup canola or vegetable oil
• 1 cup white sugar
• 1 tsp pure vanilla extract
• 1 1/4 cups canned pumpkin puree
• 2 large eggs
• 1/2 cup milk
• 1 3/4 cups all-purpose flour
• 1 tsp baking soda
• 1/2 tsp baking powder
• 1/2 tsp table salt
• 4 tsp ground pumpkin pie spice

For the cream cheese swirl:

• 8 oz cream cheese block
• 1/4 cup granulated sugar
• 1 large egg
• 1 tsp vanilla flavoring

Instructions

 

• Preheat your oven to 375 degrees Fahrenheit to ensure it reaches the right temperature for baking. Meanwhile, line your muffin pans with paper cups so they're ready for the batter.
• In a large bowl, whisk together the canola or vegetable oil, white sugar, and pure vanilla extract until fully incorporated. Add the canned pumpkin puree, eggs, and milk. Whisk until the mixture is smooth and well combined.
• In a separate bowl, mix the all-purpose flour, baking soda, baking powder, table salt, and ground pumpkin pie spice. Gradually add this dry mixture to the wet ingredients, whisking until just combined. Be careful not to overmix, which can make the muffins dense—I always stop mixing as soon as no dry spots remain.
• In a separate large bowl, beat the cream cheese block and granulated sugar together using an electric mixer until smooth and creamy. Add in the egg and vanilla flavoring, and continue mixing—scraping down the sides of the bowl as needed—until the filling is uniform. Set aside until ready to use.
• Using a #24 scoop or by filling muffin cups about 2/3 full, scoop the pumpkin muffin batter into the prepared muffin cups. Top each with a spoonful of the cream cheese filling (about a #50 scoop or a bit more than 1 tablespoon per muffin). Using a butter knife, gently fold (not swirl) the two batters together: insert the knife through the center of the muffin batter and scrape along the bottom, then draw the knife out at the edge and fold the batter back toward the center. Repeat 2 to 3 times to create a marbled effect; less mixing gives the best look.
• Bake the assembled muffins in the preheated oven at 375˚F for 15-18 minutes, or until a toothpick inserted in the center comes out with a few moist crumbs. Avoid over-baking to keep the muffins moist. Once baked, let the muffins cool completely before serving. I like to let them cool in the pan for a few minutes, then transfer them to a wire rack for best texture.