These Pumpkin Puree Cream Cheese Muffins are made with a spiced pumpkin batter and a swirl of sweetened cream cheese baked right into the center of each one.

You get a soft, moist muffin with a little pocket of tangy filling in the middle instead of a plain crumb all the way through.

I make these for fall breakfasts and after-school snacks when I want something that feels a little more special than a plain muffin but still comes together in one bowl.

They also freeze well, so I’ll usually double the batch and pull a few out as needed.

They’re perfect for fall breakfast, brunch, Thanksgiving morning, bake sales, or an easy seasonal snack with coffee or tea

If you’re into easy fall breakfasts and muffins that freeze well, these are worth bookmarking too:

Ingredients You’ll Need

Canned pumpkin puree, not pie filling, keeps the sweetness and spice level under your control in the batter. Room temperature cream cheese blends into a smooth swirl filling, cold cream cheese tends to clump instead of spreading evenly.

Ingredients

1 3/4 cups all-purpose flour
1 teaspoon baking soda
1/2 teaspoon baking powder
1/2 teaspoon salt
2 teaspoons pumpkin pie spice
1 cup canned pumpkin puree
3/4 cup brown sugar
1/2 cup vegetable oil
2 large eggs
1 teaspoon vanilla extract
4 oz cream cheese, softened
3 tablespoons granulated sugar
1/2 teaspoon vanilla extract (for filling)

Directions

Preheat the oven to 375F and line a standard 12-cup muffin tin with paper liners.
Whisk together the flour, baking soda, baking powder, salt, and pumpkin pie spice in a large bowl.
In a separate bowl, whisk the pumpkin puree, brown sugar, oil, eggs, and vanilla until smooth.
Pour the wet ingredients into the dry and stir just until combined, a few streaks of flour disappearing is fine.
Overmixing at this stage is what makes muffins turn out dense and tough instead of light, so stop as soon as the flour is worked in.
In a small bowl, beat the softened cream cheese, granulated sugar, and vanilla together until smooth.
This filling should be soft enough to swirl easily but not runny, if it feels too stiff, let it sit at room temperature a few more minutes.
Divide about two-thirds of the pumpkin batter among the 12 muffin cups.
Spoon a small dollop of the cream cheese filling into the center of each, then top with the remaining pumpkin batter, covering the filling completely.
Use a toothpick or skewer to gently swirl the cream cheese filling into the top layer of batter in each cup.
Just a couple of light swirls is enough, over-swirling mixes the filling too far into the batter and you lose the distinct pocket.
Bake for 18 to 20 minutes, until a toothpick inserted into the pumpkin batter (avoiding the cream cheese center) comes out clean.
The cream cheese center will still look soft, that’s expected, it firms up as the muffins cool.
Let the muffins cool in the tin for 5 minutes before transferring to a wire rack.
They’re fragile right out of the oven with that soft center, so give them a few minutes before moving them.
Serve warm or at room temperature and enjoy!

Important Recipe Notes

Don’t overmix the batter. Stir just until the flour disappears, overworking it develops the gluten and gives you tough, dense muffins instead of soft ones.
Use room temperature cream cheese. Cold cream cheese doesn’t swirl smoothly and tends to sit in clumps instead of spreading through the top of the muffin.
Go easy on the swirl. A couple of light passes with a toothpick is enough, too much swirling blends the filling into the batter and you lose the pocket effect.
Storage. Store in an airtight container in the fridge for up to 5 days, since these have a cream cheese filling they don’t hold as well at room temperature as a plain muffin.
Freezing. These freeze well for up to 2 months, wrap individually and thaw in the fridge overnight.
Reheating. A few seconds in the microwave brings back the soft, warm texture, especially nice with that cream cheese center.

How to Serve, Store & Customize This Recipe

Serving Serve these warm, especially the first day, when the cream cheese center is at its softest. Coffee or a warm apple cider on the side rounds out a fall breakfast nicely.

Storing Because of the cream cheese filling, keep these in the fridge in an airtight container for up to 5 days rather than at room temperature.

Customizing Add a handful of mini chocolate chips to the pumpkin batter for extra sweetness, or a streusel topping before baking for some crunch. A pinch of ground ginger in the batter adds a nice extra warmth if you want more spice.