Soft, spiced pumpkin muffins with a hidden swirl of tangy cream cheese? Yes, please. These Pumpkin Cheesecake Muffins are the perfect mashup of cozy autumn flavors and rich, creamy indulgence. Whether you’re sipping a cup of chai or brewing your morning coffee, these muffins add a warm, delightful twist to any moment of the day.

What sets these apart from other pumpkin muffins is that creamy center—a smooth, lightly sweet cheesecake filling that melts right into the tender crumb of the muffin. It’s like having your favorite pumpkin pie and cheesecake in one handheld bite. No fork required.

What Kind of Cream Cheese Works Best?

Full-fat block-style cream cheese is the best pick for this recipe. It has a thick texture and rich taste that doesn’t melt out or disappear into the batter. Avoid whipped or tub cream cheese—they contain too much air and additives, which can throw off the texture.

Let your cream cheese soften at room temperature before mixing, so it blends smoothly into the sweetened filling without lumps.

Ingredients for the Pumpkin Cheesecake Muffins

Pumpkin Puree
Canned pure pumpkin (not pumpkin pie filling) brings rich flavor and moist texture.

Cream Cheese
The heart of the cheesecake swirl. Use full-fat, block-style cream cheese for the creamiest result.

Granulated Sugar & Brown Sugar
Granulated sugar sweetens both the batter and filling. Brown sugar adds depth and a slight molasses warmth to the muffin base.

Eggs
Provide structure and moisture to both muffin batter and cream cheese layer.

All-Purpose Flour
Gives the muffins structure while keeping the texture tender.

Pumpkin Pie Spice
A warm blend of cinnamon, nutmeg, cloves, and ginger that defines the cozy flavor of these muffins.

Baking Soda
Helps the muffins rise to fluffy perfection.

Salt
Balances the sweetness and enhances the spices.

Vanilla Extract
Used in both the muffin batter and the cheesecake layer for depth and aroma.

Vegetable Oil
Keeps the muffins incredibly moist without overpowering the pumpkin flavor.

How To Make the Pumpkin Cheesecake Muffins

Step 1: Prep the Cream Cheese Filling

In a medium bowl, beat the softened cream cheese with granulated sugar, an egg yolk, and vanilla extract. Mix until the texture is smooth and creamy, then set aside. This will be the luscious cheesecake center.

Step 2: Mix the Dry Ingredients

In a large bowl, whisk together the flour, baking soda, pumpkin pie spice, and salt. This mix ensures the spices and leavening are evenly distributed throughout the batter.

Step 3: Whisk the Wet Ingredients

In a separate bowl, combine the pumpkin puree, brown sugar, granulated sugar, eggs, vegetable oil, and vanilla extract. Whisk until smooth. This will smell amazing already!

Step 4: Combine Wet and Dry

Pour the wet mixture into the bowl of dry ingredients and stir just until combined. Be careful not to overmix—a few lumps are totally fine.

Step 5: Layer and Swirl

Spoon a generous tablespoon of pumpkin batter into each lined or greased muffin cup. Add a heaping teaspoon of the cream cheese filling in the center. Top with another tablespoon of pumpkin batter. Use a toothpick to gently swirl the top layer for a marbled effect.

Step 6: Bake and Cool

Bake at 350°F (175°C) for 18-22 minutes, or until the tops are set and a toothpick inserted into the muffin part comes out clean. Let them cool in the pan for 5 minutes, then transfer to a wire rack.

How to Serve and Store These Muffins

These muffins are perfect served slightly warm or at room temperature. That creamy center tastes like a surprise cheesecake bite tucked into a pumpkin dream.

For a bakery-style experience, try sprinkling a bit of cinnamon sugar on top just before baking.

To store, let muffins cool completely and place in an airtight container. They’ll keep at room temperature for 2 days, or refrigerate for up to 5 days. For longer storage, freeze them in a zip-top bag and thaw at room temp overnight.

Frequently Asked Questions

How do I know when the muffins are done?

Insert a toothpick into the pumpkin portion of the muffin (not the cheesecake center). It should come out clean or with just a few moist crumbs.

Can I use homemade pumpkin puree?

Yes, just make sure it’s not too watery. Blot it with a paper towel if needed to get the same consistency as canned pumpkin.

What’s the best way to swirl the cheesecake layer?

A toothpick or skewer works best. Don’t over-swirl—you want visible layers and contrast.

Can I make these ahead of time?

Absolutely. They’re actually even better the next day once the flavors settle. Store them in the fridge or freeze for future treats.

Can I make them gluten-free?

Yes, just use a 1:1 gluten-free flour blend. The texture may vary slightly but they still bake beautifully.

Do they need to be refrigerated?

If you’re storing them longer than 2 days, yes. The cream cheese center makes them best kept chilled for freshness.

Want More Muffin Ideas with a Twist?

If you adore the fall vibes in these Pumpkin Cheesecake Muffins, try a few more of our cozy creations:

Easy Pumpkin Muffins for a simpler, classic option.
Lemon Raspberry Swirl Cheesecake Cups if you’re craving bright and creamy.
Condensed Milk Snow Cookies that practically melt in your mouth.
Caramel Cheesecake Cookies for more cheesecake-meets-cookie goodness.
Shamrock Mint Milkshake Pie if you want a festive dessert with a creamy twist.

For even more creative bakes, check out my Pinterest board here—I post new ideas almost daily!

📌 Save this recipe to your Pinterest dessert board so you can come back to it any time.

And let me know in the comments how yours turned out. Did you add a cinnamon sugar topping or switch up the filling? Maybe even used a gluten-free twist?

I love seeing how you personalize these treats. Got questions? Drop them below so we can all bake smarter together.