Pumpkin Cheesecake Muffins

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When fall rolls in and pumpkins take over the shelves, I know it’s time to bring out one of my favorite seasonal bakes—Pumpkin Cheesecake Muffins. These warm, spiced treats are everything I love about autumn packed into a single bite. The best part? That luscious swirl of creamy cheesecake right in the middle that makes every muffin feel like a little indulgent surprise.

I started making these muffins years ago as a way to combine my love for classic pumpkin spice and creamy cheesecake, and they’ve become a staple in my kitchen ever since. Whether I’m serving them as a cozy breakfast option, a sweet afternoon snack, or even a simple dessert after dinner, they always manage to disappear quickly. If you’re looking for a muffin that hits all the comforting notes of fall while delivering bakery-style flavor, this one’s for you.

Why You’ll Love These Pumpkin Cheesecake Muffins

These muffins are a beautiful balance of moist pumpkin spice cake and tangy, rich cheesecake filling. They’re easy to make and deliver that perfect café-style experience without leaving your kitchen. Plus, they look impressive enough to serve for brunch or bring to a gathering, but don’t require any fancy equipment or advanced baking skills.

What Makes the Cheesecake Swirl So Special?

That creamy center isn’t just a visual treat—it brings an irresistible texture contrast to the muffin. The tanginess of the cream cheese pairs beautifully with the warm spices in the pumpkin batter, making every bite complex and satisfying. I like to pipe the cream cheese in the center and swirl just a bit for a marbled effect on top, which gives the muffins that bakery-finish look.

Can I Make These with Other Types of Puree?

Absolutely! While pumpkin puree is traditional and gives the muffins their signature flavor, you can substitute it with sweet potato puree or even mashed butternut squash. Just make sure your substitute is thick and not watery—otherwise the texture of the batter might get thrown off.

Options for Substitutions

• Dairy-Free: Use a dairy-free cream cheese alternative and a plant-based milk.
• Gluten-Free: A 1:1 gluten-free flour blend works well in place of all-purpose flour.
• Sugar Swaps: Coconut sugar or maple sugar can be used instead of granulated sugar for a richer, more caramelized flavor.
• Spice Variation: If you don’t have pumpkin pie spice, you can use a mix of cinnamon, nutmeg, ginger, and cloves.
• Add-ins: Try folding in chopped pecans, walnuts, or even chocolate chips to add texture and depth.

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Ingredients for These Pumpkin Cheesecake Muffins

• Pumpkin Puree – The base of the muffin, bringing moisture, natural sweetness, and rich pumpkin flavor.
• All-Purpose Flour – Provides structure and stability for the muffin batter.
• Granulated Sugar – Sweetens the muffins while balancing the tang of the cheesecake swirl.
• Brown Sugar – Adds a deeper, molasses-like sweetness that complements the spices.
• Vegetable Oil – Keeps the muffins moist and tender without overpowering the flavor.
• Eggs – Help bind the ingredients together and add structure.
• Baking Powder & Baking Soda – Work together to help the muffins rise and become fluffy.
• Salt – Enhances all the other flavors and balances the sweetness.
• Pumpkin Pie Spice – A cozy blend of cinnamon, nutmeg, ginger, and cloves that defines the flavor of these muffins.
• Vanilla Extract – Adds warmth and rounds out both the pumpkin and cheesecake flavors.
• Cream Cheese – The heart of the cheesecake swirl, bringing a tangy, creamy contrast.
• Powdered Sugar – Used to sweeten the cream cheese without making it grainy.

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Step 1: Prepare the Cream Cheese Filling

In a small mixing bowl, beat softened cream cheese with powdered sugar and a splash of vanilla extract until smooth and creamy. Set aside while you make the muffin batter.

Step 2: Mix the Dry Ingredients

In a large bowl, whisk together all-purpose flour, baking powder, baking soda, salt, and pumpkin pie spice. Make sure the spices are evenly distributed so you don’t end up with pockets of intense flavor.

Step 3: Combine the Wet Ingredients

In a separate bowl, combine pumpkin puree, granulated sugar, brown sugar, eggs, vegetable oil, and vanilla extract. Mix well until fully combined and smooth.

Step 4: Combine Wet and Dry Mixtures

Gradually add the dry ingredients to the wet mixture, stirring until just combined. Don’t overmix, or the muffins may come out dense instead of tender.

Step 5: Fill the Muffin Tins

Line a muffin tin with paper liners or lightly grease the cups. Fill each cup about 2/3 full with pumpkin batter. Then spoon about a tablespoon of the cream cheese filling into the center of each muffin. Swirl gently with a toothpick or knife for a marbled effect.

Step 6: Bake

Bake the muffins at 350°F (175°C) for 18–22 minutes, or until a toothpick inserted into the pumpkin part (not the cheesecake center) comes out clean. The tops should be golden and slightly domed.

Step 7: Cool and Enjoy

Let the muffins cool in the tin for 5 minutes, then transfer to a wire rack to cool completely. This helps the cheesecake center set properly and ensures the best texture.

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How Long to Prepare Pumpkin Cheesecake Muffins

Making these muffins is surprisingly quick for how indulgent they taste. Most of the time is hands-off while they bake or cool. Here’s how the timeline breaks down:

Prep Time: Preparing both the pumpkin batter and the cream cheese filling will take around 15–20 minutes. If your cream cheese is already softened, it goes even faster. This includes mixing, assembling the muffins, and swirling in the cheesecake.

Bake Time: They typically bake in about 18–22 minutes in a preheated oven at 350°F (175°C). Once done, you’ll need about 5 minutes of resting time in the pan before transferring them to a cooling rack.

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Tips for Perfect Pumpkin Cheesecake Muffins

• Use room temperature cream cheese for a smooth, lump-free filling.
• Don’t overmix the batter—stop as soon as the dry ingredients are incorporated to avoid tough muffins.
• Swirl gently with a toothpick for a pretty marbled effect without blending the layers completely.
• Use pumpkin puree, not pumpkin pie filling. The latter is pre-sweetened and spiced, which will throw off your flavor balance.
• Line your muffin tin to avoid sticking and make cleanup a breeze.

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Watch Out for These Mistakes While Cooking

• Cold cream cheese will make the filling clumpy and hard to swirl.
• Overfilling the muffin tins can cause the batter to spill over and ruin the shape.
• Underbaking will leave the cheesecake centers too gooey and unset.
• Not checking the doneness in the right spot—insert the toothpick in the muffin portion, not the cheesecake swirl.
• Using watery pumpkin puree (often homemade) can make the batter too thin.

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What to Serve With Pumpkin Cheesecake Muffins?

1. Hot Chai Latte

The warm spices of chai pair beautifully with the pumpkin and cinnamon flavors in the muffins.

2. Greek Yogurt Parfait

Balance the sweetness with a light and tangy yogurt bowl topped with granola.

3. Scrambled Eggs and Greens

For a savory counterpoint, serve with a plate of fluffy scrambled eggs and sautéed spinach.

4. Apple Slices and Almond Butter

A crunchy, healthy side that brings in even more fall flavor.

5. Vanilla Ice Cream

If you’re serving these as dessert, a scoop of vanilla ice cream alongside a warm muffin is perfection.

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Storage Instructions

Room Temperature: Store cooled muffins in an airtight container for up to 2 days. Because of the cream cheese, it’s safest to refrigerate them after that point.

Refrigerator: Keep muffins in an airtight container in the fridge for up to 5–6 days. Let them sit at room temp or microwave briefly before serving for best texture.

Freezer: Freeze muffins individually wrapped in plastic wrap and then placed in a freezer bag for up to 2 months. Thaw overnight in the fridge or microwave on low to reheat.

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Estimated Nutrition (Per Muffin)

• Calories: ~240 kcal
• Protein: 4g
• Carbohydrates: 28g
• Sugar: 16g
• Fat: 12g
• Saturated Fat: 4.5g
• Fiber: 1g
• Sodium: 190mg
• Cholesterol: 35mg

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Frequently Asked Questions

Can I make these muffins ahead of time?

Yes! They’re perfect for prepping the day before. Just store them in the fridge and bring to room temperature before serving.

Can I double the recipe?

Absolutely. Just be sure not to overcrowd the muffin tins—bake in batches if needed.

Can I use homemade pumpkin puree?

Yes, but make sure it’s very thick. If it’s watery, strain it through cheesecloth to avoid a soggy batter.

Are these muffins freezer-friendly?

Very much so. Wrap them tightly and freeze for up to 2 months. Reheat in the microwave or let thaw at room temp.

What can I use instead of powdered sugar in the cream cheese?

You can blend granulated sugar until fine, or use maple syrup for a slightly different sweetness and flavor.

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Conclusion

Pumpkin Cheesecake Muffins are the kind of treat that feels cozy, festive, and just the right amount of indulgent. With warm spices, creamy centers, and a tender crumb, they’re everything I want in a fall bake. Whether you enjoy them with coffee in the morning or as a sweet end to your day, they’re guaranteed to bring smiles and maybe even requests for seconds. Don’t be surprised if they become a seasonal staple in your kitchen too.

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