These Pumpkin Cream Cheese Muffins use my go-to pumpkin muffin base that bakes up soft with just enough structure to keep the creamy filling right in the center. Warmly spiced and easy to make, they're one of my favorite fall baking recipes.

Two pumpkin muffins with creamy centers stacked on parchment paper, with cinnamon sticks in the background.

A woman with medium-length dark brown hair and fair skin smiling with trees behind her.

Note from Erin

I've been baking pumpkin muffins for my family for years, and they've always been an autumn favorite in our house.

When my kids discovered the Starbucks version with the cream cheese center, they immediately asked if I could make something similar at home. Since I love pumpkin and am obsessed with cheesecake, I gladly obliged.

I tested a few recipes online, but in the end, I went back to my own tried-and-true pumpkin muffin base and added a touch of sweet cheesecake filling.

Helpful Ingredient Tips

The recipe card at the bottom of this post includes the complete list of ingredients, measurements, and instructions.

Baking ingredients including eggs, flour, pumpkin, oil, spices, cream cheese, sugar, and vanilla on a table.

Flour – I use a little more flour than most cream cheese pumpkin muffin recipes. It gives the batter enough structure to hold the filling right in the center instead of letting it sink, and the muffins still stay tender thanks to the whipped eggs that add lightness to the batter.
Pumpkin Puree – Brands can vary in moisture, so if your pumpkin looks especially wet, blot it with paper towels before adding it to the batter. Too much moisture can make the muffins gummy instead of fluffy.
Cream Cheese – For the smoothest filling, start with full-fat cream cheese that’s completely softened. If it’s still cool, the filling won’t blend evenly and can look grainy after baking.

Tips to Make the Best Pumpkin Cream Cheese Muffins

A glass bowl with flour and spices on the left, and flour blended with spices on the right.

Whisk Dry Ingredients

I like to whisk a little longer than feels necessary. It makes a difference in how evenly the spices spread through the batter, so you don't end up with one muffin that tastes mostly of cloves.
If you aren't measuring with a scale, give your flour a quick fluff with a fork and gently spoon it into the measuring cup.

Glass bowl with pale batter on the left and orange batter on the right, divided down the middle.

Beat Wet Ingredients

I always start the mixer on low for a few seconds so the sugar doesn't fly everywhere, then work my way up to medium-high once it starts to thicken.
When it's time to add the oil and pumpkin, keep the speed low and mix just until everything comes together. Overmixing here can deflate all that fluffy air you just worked to build.

Glass mixing bowl with pumpkin batter, half with flour on top and half fully mixed, on a light surface.

Mix in the Flour

When the flour goes in, the goal is to combine, not to smooth it out completely. I stop mixing while there is still a little flour left, then stir that in by hand.
The batter should be similar in thickness to brownie batter.

A bowl of creamy frosting and a piping bag filled with frosting on a light gray surface.

Make Cream Cheese Filling

If you forget to soften your cream cheese (I do all the time), unwrap it, cut it into cubes, and microwave it for 10-15 seconds.

Two muffin pans with orange batter in cupcake liners; one side shows filling, the other has white dollops on top.

Fill Muffin Cups

Using a large cookie scoop (#20) to portion the batter keeps things tidy and makes every muffin the same size.
When you pipe in the cream cheese, push the tip down just a little so the filling sits in the center instead of floating on top.

Top Tip!

Whip the eggs and sugar until they're pale and drip in thick ribbons when you pull out the beater. That extra air keeps the muffins soft and helps them rise tall instead of sinking around the cream cheese center.

The tops of cheesecake pumpkin muffins should look puffed and slightly springy when touched, and the filling should appear set and just barely glossy. If you test with a toothpick, check the pumpkin part, not the center, or you'll hit the creamy filling and think they're underbaked.

Plate of pumpkin cream cheese muffins with a swirl in the center, surrounded by spices and a striped cloth.

Make it Special✨

Sprinkle a few pepitas on top before baking for that bakery-style look. They toast up golden and add a light crunch that makes the pumpkin spice muffins feel a little extra special.

Note from Erin

Helpful Ingredient Tips