If you are a fan of cozy autumn baking, you simply have to try these Pumpkin Cream Cheese Muffins. Imagine the very best soft, pumpkin-spiced muffin you’ve ever had, now picture it with a creamy, cheesecake-like filling in the center and a bakery-ready swirl on top. That’s exactly what you get with this recipe: flavor-packed, moist muffins layered with rich cream cheese – like all the best parts of fall in a single bite. They’re so much better than any coffee shop version, effortless to make at home, and guaranteed to be a hit!

Pumpkin Cream Cheese Muffins Recipe - Recipe Image

Ingredients You’ll Need

What makes these Pumpkin Cream Cheese Muffins stand out is the beautiful balance of warm spices, luscious pumpkin, and silky cream cheese—all using simple ingredients you likely already have in your kitchen. Each plays a big part in the muffin’s irresistible appeal and texture.

Pumpkin Puree: The star ingredient—be sure to use pure pumpkin puree, not pumpkin pie filling, for the richest flavor and perfect moisture.
Light Brown Sugar: Adds a caramel note that deepens the flavor and helps create that ultra-soft, tender crumb.
Granulated Sugar: Brings a clean sweetness that balances the tang of the cream cheese and enhances the overall taste.
Eggs: Bind everything together for a delicate, pillowy muffin; room temperature eggs help your batter blend evenly.
Sunflower Oil: Gives these muffins lightness and a super-moist texture—neutral in flavor, so nothing overpowers the pumpkin!
Pure Vanilla Extract: Rounds out the flavors and adds gentle, fragrant warmth to both the muffin batter and the cream cheese filling.
All-Purpose Flour: The source of structure, keeping everything held together without weighing down the muffins.
Pumpkin Pie Spice: Brings all the autumn magic—cinnamon, nutmeg, ginger, and cloves in one swoop; use homemade or store-bought!
Cinnamon: A little extra for an aromatic kick that brightens the pumpkin.
Baking Powder & Baking Soda: The leavening duo that ensures your muffins rise tall and fluffy.
Salt: Just a touch to enhance every other flavor in these Pumpkin Cream Cheese Muffins.
Whole Milk: Keeps the crumb moist and tender, never dry.
Cream Cheese: Full-fat, at room temperature for easy mixing, gives you a truly decadent filling.
Addition of Sugar, Flour, and Vanilla (for Cream Cheese Filling): Blends with the cream cheese to give it perfect sweetness, set texture, and just the right consistency for piping.
Chopped Pumpkin Seeds (optional): For a beautiful, bakery-worthy crunch and a little extra visual flair!

How to Make Pumpkin Cream Cheese Muffins

Step 1: Prep Your Tools and Oven

Start by preheating your oven to 425°F, and line a standard 12-cup muffin pan with non-stick liners (I always pick parchment liners—they keep the muffins from sticking and make cleanup a breeze). Having everything in place before you start mixing means you’re set for muffin success from the get-go.

Step 2: Whisk Together the Pumpkin Muffin Batter

Combine the pumpkin puree and both types of sugar in a large mixing bowl. Whisk them together until the mixture is smooth and glossy — this not only makes your muffins moist but also starts dissolving the sugar for an even crumb. Stir in the eggs, oil, and vanilla extract, blending until it’s all wonderfully silky.

Step 3: Mix Dry Ingredients Separately

In a separate bowl, whisk together the all-purpose flour, pumpkin pie spice, cinnamon, baking powder, baking soda, and salt. This step ensures that the spices and leaveners are distributed evenly, so every bite of your Pumpkin Cream Cheese Muffins is perfectly spiced and rises evenly.

Step 4: Combine Wet and Dry Mixes

Gently fold the dry ingredients into the wet pumpkin mixture, but pause before it’s completely combined. Add the whole milk and finish folding until everything is just mixed (a few lumps are totally fine, as long as you don’t see dry flour). At this point, cover the bowl and let the batter rest at room temperature for 30 minutes. This simple trick results in taller, fluffier muffins every time!

Step 5: Prepare the Cream Cheese Filling

While the batter rests, make the creamy filling. Beat the softened cream cheese with sugar, flour, vanilla extract, and milk in a small bowl until super smooth—no lumps allowed! Transfer this luscious mixture to a piping bag or a zip-top bag, snipping the corner when you’re ready to use. The filling should be thick but pipeable, like a soft frosting.

Step 6: Assemble the Muffins

Divide the rested batter evenly among the muffin cups—they should be filled to the rim. Take your prepared piping bag and insert the tip about a quarter-inch into the center of each muffin. Gently squeeze to swirl the cream cheese filling at the top, about a one-inch circle. Use up all the filling (about half a tablespoon in each). If you want, sprinkle chopped pumpkin seeds around the muffin tops for pretty crunch—just avoid covering the cream cheese swirl.

Step 7: Bake to Perfection

Pop the tray in your preheated oven at 425°F for 5 minutes to help the muffins rise tall, then lower the temperature to 350°F and bake for another 12 to 15 minutes. They’re done when the tops feel just firm and a toothpick comes out clean (watch out for a little melted cream cheese on the tester!). Cool for 5 minutes in the pan, then transfer each muffin to a wire rack to finish cooling—if you can wait that long!

How to Serve Pumpkin Cream Cheese Muffins

Garnishes

The simplest way to garnish these beauties is with a shower of chopped pumpkin seeds right before baking. For extra autumn wow-factor, dust the cooled muffins lightly with powdered sugar or a hint of cinnamon. If you’re feeling creative, a drizzle of maple glaze makes them truly next-level.

Side Dishes

Pumpkin Cream Cheese Muffins are so deliciously satisfying on their own, but they also shine with a side of crisp apple slices, a glass of chai tea, or your favorite hot coffee. For a sweet brunch spread, pair them with yogurt and fresh fruit for the coziest fall morning ever.

Creative Ways to Present

If you’re entertaining, arrange the muffins on a rustic wooden board with mini pumpkins and cinnamon sticks for a harvest vibe. Or, serve each muffin on a small plate with a swirl of whipped cream and a sprinkling of pumpkin seeds on top for that special café-style touch. They also look extra cute tucked into a parchment-lined basket for easy grab-and-go treats.

Make Ahead and Storage

Storing Leftovers

To keep your Pumpkin Cream Cheese Muffins moist and fresh, store them in an airtight container at room temperature for up to two days. If your kitchen is warm, pop them in the fridge—just bring to room temp before eating for the best flavor and fluffy texture.

Freezing

These muffins freeze beautifully! Just wrap each cooled muffin in plastic wrap and place in a zip-top bag or airtight container. They’ll stay perfectly tender and moist in the freezer for up to three months, ready whenever you crave a pumpkin treat.

Reheating

Pop a muffin (unwrapped) in the microwave for 10-20 seconds, just until the center is soft and the cream cheese lightly warmed. Or, reheat gently in a low oven (about 300°F) for 5-7 minutes—your kitchen will smell like a bakery all over again!

FAQs

Can I use homemade pumpkin puree instead of canned?

Absolutely! Just be sure your puree is thick and not watery—homemade pumpkin often needs to be blotted or drained before using. This ensures your Pumpkin Cream Cheese Muffins stay fluffy instead of soggy.

Can I make these muffins gluten-free?

Yes! Substitute your favorite 1:1 gluten-free baking flour for the all-purpose flour, and check that your cream cheese and other ingredients are gluten-free. You’ll still get moist, bakery-worthy muffins bursting with pumpkin flavor.

How do I prevent the cream cheese filling from sinking?

Be sure to pipe the filling just below the muffin batter’s surface and not too deep in the middle. This keeps the cream cheese swirl visible and beautifully centered on top when baking.

Can I double the recipe to make more muffins?

Definitely—this recipe doubles easily. Just use two muffin pans and rotate them halfway through baking if your oven doesn’t heat evenly. More Pumpkin Cream Cheese Muffins means more smiles to share!

What can I use instead of pumpkin seeds for topping?

If you’re not a fan of pumpkin seeds, try chopped pecans, walnuts, or even a sprinkle of coarse turbinado sugar for sparkle and crunch. Or, skip toppings altogether for a classic, creamy finish.

Final Thoughts

If you’re looking for a fall baking project that guarantees rave reviews, give these Pumpkin Cream Cheese Muffins a spot at your table. Every bite is a little swirl of spice, pumpkin, and creamy tang—so comforting and so easy to love. I hope you have as much fun baking them as you do sharing (or savoring!) them. Happy baking!