Pumpkin Cheesecake Muffins – Moist, Spiced, and Creamy in Every Bite
If you love pumpkin season as much as we do, these Pumpkin Cheesecake Muffins will be your new favorite fall treat. Imagine the warm, cozy flavors of pumpkin spice swirled together with a creamy cheesecake filling — all baked into soft, tender muffins that smell like autumn itself.
These bakery-style muffins have the perfect balance of sweet pumpkin and tangy cream cheese, with a texture that’s moist and fluffy every time. Whether you’re making them for breakfast, dessert, or a cozy afternoon snack, they bring all the comforting flavors of pumpkin pie and cheesecake in one irresistible bite.
They’re simple to make, look gorgeous with that signature cheesecake swirl, and taste even better than your favorite coffee shop version — plus, you can make them right in your own kitchen.
Why You’ll Love These Pumpkin Cheesecake Muffins
1. Bakery-style look and flavor
Soft, tall muffins with creamy cheesecake centers and that classic swirl on top.
2. Simple ingredients
No fancy tools or techniques — just mix, fill, and bake.
3. Perfectly spiced
Made with pumpkin puree and warm spices for a cozy, seasonal flavor.
4. Moist and tender texture
Thanks to the pumpkin and oil, these muffins stay soft for days.
5. Make-ahead friendly
They store and freeze beautifully, so you can enjoy them anytime.
6. Great for fall gatherings
Perfect for breakfast spreads, bake sales, or Thanksgiving desserts.
What You’ll Need
For the Pumpkin Muffin Batter:
- 1 3/4 cups all-purpose flour
- 1 teaspoon baking soda
- 1/2 teaspoon baking powder
- 1/2 teaspoon salt
- 1 1/2 teaspoons ground cinnamon
- 1/2 teaspoon ground nutmeg
- 1/4 teaspoon ground ginger
- 1/4 teaspoon ground cloves
- 1 cup pumpkin puree (not pumpkin pie filling)
- 2/3 cup granulated sugar
- 1/3 cup brown sugar, packed
- 2 large eggs
- 1/2 cup vegetable oil (or melted coconut oil)
- 1/4 cup milk (dairy or non-dairy)
- 1 teaspoon pure vanilla extract
For the Cheesecake Filling:
- 6 ounces cream cheese, softened
- 3 tablespoons granulated sugar
- 1 teaspoon vanilla extract
- 1 egg yolk
For the Topping (Optional):
- Coarse sugar or streusel crumble for a bakery-style finish
Step-by-Step Instructions
Step 1: Preheat and Prepare
Preheat your oven to 350°F (175°C).
Line a 12-cup muffin tin with paper liners or lightly grease it.
This helps the muffins release easily and keeps them moist as they bake.
Step 2: Make the Cheesecake Filling
In a small bowl, beat the softened cream cheese with sugar, vanilla, and egg yolk until smooth and creamy.
Set aside — this will be swirled into your pumpkin batter later.
Tip: For the smoothest swirl, make sure your cream cheese is at room temperature.
Step 3: Mix the Dry Ingredients
In a medium mixing bowl, whisk together the flour, baking soda, baking powder, salt, cinnamon, nutmeg, ginger, and cloves until evenly combined.
This ensures all the spices are distributed and gives the muffins that warm fall aroma.
Step 4: Combine the Wet Ingredients
In a large bowl, whisk together pumpkin puree, granulated sugar, brown sugar, eggs, oil, milk, and vanilla until smooth and well blended.
Step 5: Combine Wet and Dry
Add the dry ingredients to the wet ingredients and stir just until no dry streaks remain.
Be careful not to overmix — this keeps the muffins soft and fluffy.
The batter should be thick and smooth.
Step 6: Fill the Muffin Cups
Spoon about 1 1/2 tablespoons of pumpkin batter into each muffin cup.
Then add about 1 tablespoon of cheesecake filling on top.
Finish with another tablespoon of pumpkin batter, filling each cup about 3/4 full.
For a pretty swirl:
Use a toothpick or small knife to gently swirl the cheesecake layer into the pumpkin batter.
Optional: Sprinkle each muffin with coarse sugar or streusel topping for extra texture.
Step 7: Bake the Muffins
Bake for 18–22 minutes, or until the tops are set and a toothpick inserted near the edge (not the cheesecake center) comes out clean.
The centers will still look slightly soft — that’s perfect.
Let muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
Tips for Perfect Pumpkin Cheesecake Muffins
- Use room temperature cream cheese.
Cold cream cheese won’t blend smoothly and can cause lumps in your swirl. - Don’t overmix the batter.
Mix until just combined to keep your muffins tender. - Use pumpkin puree, not pie filling.
Pure pumpkin gives the right consistency and allows you to control the sweetness. - Create a defined swirl.
Drag your toothpick gently — too much swirling can mix the batters completely. - Cool completely before storing.
The cheesecake layer needs time to set as they cool.
Flavor Variations
Once you’ve tried the classic version, here are some fun ways to switch it up:
Pumpkin Chocolate Chip Cheesecake Muffins
Add 1/2 cup mini chocolate chips to the pumpkin batter.
Maple Pumpkin Muffins
Replace half of the granulated sugar with pure maple syrup for rich flavor.
Cinnamon Streusel Pumpkin Muffins
Top with a simple streusel made from butter, brown sugar, flour, and cinnamon before baking.
Nutty Pumpkin Muffins
Add chopped pecans or walnuts to the batter for crunch.
Gluten-Free Option
Use a gluten-free 1:1 baking flour blend — the texture stays moist and tender.
Serving Suggestions
These Pumpkin Cheesecake Muffins are delicious at room temperature or slightly chilled.
Serve them for:
- Breakfast or brunch: Pair with hot coffee or a pumpkin spice latte.
- Afternoon snack: Perfect with tea or cider.
- Dessert: Top with whipped cream or a drizzle of caramel sauce.
- Holiday spread: Add them to your Thanksgiving dessert table for a lighter option than full cheesecake.
They’re moist enough to enjoy on their own, but the creamy center makes them extra special without needing any frosting.
How to Store and Reheat
At Room Temperature:
Store cooled muffins in an airtight container for up to 2 days.
If your kitchen is warm, refrigerate instead.
Refrigerator:
Keep in a sealed container for up to 5 days.
The cheesecake layer stays firm and delicious when chilled.
Freezer:
Wrap muffins individually in plastic wrap, then store in a freezer bag for up to 2 months.
Thaw overnight in the fridge or microwave for 20–30 seconds before serving.
Make-Ahead Option
You can make both the pumpkin batter and cheesecake filling a day in advance.
Store them separately in the fridge, then assemble and bake the next day.
For freezer meal prep, bake and cool the muffins, then freeze them individually — great for grab-and-go breakfasts all season long.
Troubleshooting
Muffins are dense:
Overmixing the batter can deflate the texture — stir only until combined.
Cheesecake filling sinks:
Try using slightly thicker cheesecake filling (add a teaspoon of flour) or don’t swirl too deeply.
Muffins too dry:
Make sure you’re using pure pumpkin puree and not overbaking.
Cheesecake layer too soft:
Let the muffins cool fully before serving — the filling firms up as it sets.
Frequently Asked Questions
Can I use low-fat cream cheese?
Yes, but full-fat gives a richer flavor and creamier texture.
Can I make these without eggs?
You can try using flax eggs (1 tablespoon flaxseed meal + 3 tablespoons water per egg), though the texture will be slightly denser.
Can I make them dairy-free?
Use dairy-free cream cheese and plant-based milk for a great alternative.
Can I add frosting on top?
They don’t need it, but a drizzle of cream cheese glaze or caramel is delicious.
Do I need muffin liners?
Liners make cleanup easier, but you can grease the pan well instead.
Nutrition Information (Approximate per Muffin)
- Calories: 230
- Protein: 4g
- Fat: 11g
- Carbohydrates: 28g
- Fiber: 1g
- Sugar: 17g
(Nutrition values may vary depending on brands and optional toppings.)
Why This Recipe Works
The secret to these Pumpkin Cheesecake Muffins is the contrast — moist, spiced pumpkin batter combined with creamy, tangy cheesecake. The pumpkin puree keeps the muffins soft for days, while the cream cheese adds richness without overpowering sweetness.
The swirl also helps the muffins bake evenly — the creamy center locks in moisture, giving every bite a melt-in-your-mouth texture. The result is a perfectly balanced fall treat: sweet, creamy, and warmly spiced.
Tips for Customizing Your Muffin Routine
- Make mini versions.
Use a mini muffin tin and reduce baking time to 12–14 minutes — perfect bite-sized treats. - Create a muffin bar.
Serve alongside other fall muffins like apple cinnamon or maple pecan for a cozy spread. - Double the batch.
Freeze half so you’ll always have a quick fall breakfast or dessert ready. - Top with cream cheese frosting.
For a dessert-style version, spread a little frosting once cooled. - Add a crunch.
Sprinkle with pumpkin seeds, oats, or pecans before baking for texture.
Final Thoughts
These Pumpkin Cheesecake Muffins bring together everything we love about fall — pumpkin spice, creamy cheesecake, and the comforting smell of home baking.
They’re soft, rich, and perfectly balanced with just the right sweetness and spice. Whether you’re baking them for breakfast, brunch, or dessert, they’re guaranteed to impress and disappear quickly.
Simple to make, beautiful to serve, and absolutely irresistible — these muffins are a must-bake for pumpkin season.
Homemade fall treats don’t get cozier than this.