Pumpkin Cheesecake Muffins Recipe
If you’re dreaming of a cozy treat that combines the warm spices of autumn with the rich creaminess of cheesecake, these Pumpkin Cheesecake Muffins are about to become your new favorite. Moist pumpkin-infused muffin bases meet luscious swirls of dreamy cheesecake filling in every bite, creating a harmonious flavor and texture that feels like a hug from the inside. Whether you’re baking for a brunch spread, a holiday gathering, or just because, these Pumpkin Cheesecake Muffins bring a perfect balance of spice, sweetness, and tang that’s impossible to resist.

Ingredients You’ll Need
The magic of these Pumpkin Cheesecake Muffins comes from a handful of simple ingredients that you probably already have in your pantry. Each item plays a crucial role in perfecting the taste, texture, and that enchanting fall color we all love. From fluffy flour and fragrant spices to silky cream cheese and velvety pumpkin puree, every component works together for maximum flavor impact.
- 1 ½ cups all-purpose flour: Provides the sturdy base that holds the muffins together while keeping them tender.
- 1 cup sugar: Adds sweetness and helps create a lovely golden brown crust.
- 1 tsp baking powder: Gives the muffins a light, airy rise.
- ½ tsp baking soda: Enhances rise and helps balance acidity for perfect texture.
- 1 tsp cinnamon: Infuses that classic warm spice essential in pumpkin desserts.
- ½ tsp nutmeg: Adds a subtle nutty warmth to complement the pumpkin.
- ½ tsp salt: Balances the flavors and enhances sweetness.
- ½ cup vegetable oil: Keeps the muffins moist and tender.
- 2 eggs: Bind the ingredients and add richness.
- 1 cup pumpkin puree: The star ingredient that brings moisture, color, and that unmistakable fall flavor.
- 1 tsp vanilla extract: Rounds out the profile with sweet floral notes.
- 8 oz cream cheese, softened: For the luscious creamy cheesecake filling.
- ¼ cup sugar: Sweetens the cheesecake filling to perfection.
- 1 egg: Adds structure to the cheesecake swirl.
- 1 tsp vanilla extract: Enhances the creamy richness of the filling.
How to Make Pumpkin Cheesecake Muffins
Step 1: Preheat Your Oven
Everything starts with the perfect oven temperature. Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners. This ensures your muffins bake evenly and come out with a beautiful shape.
Step 2: Prepare the Muffin Batter
In a medium bowl, whisk together the all-purpose flour, sugar, baking powder, baking soda, cinnamon, nutmeg, and salt. In a separate large bowl, combine the vegetable oil, eggs, pumpkin puree, and vanilla extract. Then, gently fold the dry ingredients into the wet mixture until just combined—be careful not to overmix, or you risk tough muffins. The batter should be thick, smooth, and full of autumn goodness.
Step 3: Make the Cheesecake Filling
In another bowl, beat together the softened cream cheese, ¼ cup sugar, egg, and vanilla extract until the mixture is smooth and creamy. This luscious filling will give these muffins that decadent cheesecake swirl in every bite—absolutely worth every extra spoonful!
Step 4: Assemble the Muffins
Here’s where the magic happens. Fill each muffin liner halfway with the pumpkin batter, then add a generous spoonful of the cheesecake filling on top. Finally, cover the cream cheese layer with more pumpkin batter until the liners are about three-quarters full. This layering creates a beautiful marbled effect once baked.
Step 5: Bake to Perfection
Bake your muffins for 20 to 25 minutes, or until a toothpick inserted through the center comes out clean. Let your Pumpkin Cheesecake Muffins cool in the pan for about 5 minutes before transferring them to a wire rack. This little bit of patience lets them set nicely and makes them easier to handle.
How to Serve Pumpkin Cheesecake Muffins

Garnishes
Sprinkle a bit of powdered sugar over the tops or add a dollop of whipped cream for a pretty and tasty touch. You can also top with a few crushed gingersnap cookies or chopped pecans to add texture and a nutty contrast.
Side Dishes
Pair these Pumpkin Cheesecake Muffins with a steaming cup of coffee, a chai latte, or a rich hot chocolate for the ultimate cozy combo. Adding a fruit salad or fresh sliced apples with a drizzle of honey can balance the richness with a refreshing brightness.
Creative Ways to Present
Try slicing a warm muffin horizontally and spreading a little extra cream cheese or cinnamon butter in the middle for a decadent snack. Alternatively, turn these into a dessert parfait layered with whipped cream and caramel sauce for a playful twist that will impress guests.
Make Ahead and Storage
Storing Leftovers
Keep your Pumpkin Cheesecake Muffins fresh by storing them in an airtight container at room temperature for up to 2 days. If you want to extend their life, refrigeration for up to a week is a great option, just bring them to room temp or warm slightly before enjoying.
Freezing
These muffins freeze wonderfully. Simply wrap each muffin individually in plastic wrap and place in a freezer-safe bag or container. They can be stored for up to 3 months. Thaw overnight in the refrigerator or at room temperature for a soft and delicious treat anytime.
Reheating
To bring your muffins back to their just-baked glory, warm them in the microwave for 15-20 seconds or pop them in a preheated oven at 300°F (150°C) for about 5-7 minutes. This will revive the cream cheese swirl and pumpkin batter flavors beautifully.
FAQs
Can I use canned pumpkin puree for these muffins?
Absolutely! Canned pumpkin puree is perfect for this recipe and provides consistent moisture and flavor, making the process effortless.
Can I substitute cream cheese with something else?
You could try mascarpone or ricotta cheese for a different twist, but cream cheese provides that classic tang and creaminess crucial to the filling’s signature taste.
Are these muffins gluten-free?
The recipe as written uses all-purpose flour, so it’s not gluten-free. However, you can substitute with a gluten-free flour blend designed for baking to make a tasty gluten-free version.
How long do these muffins stay fresh?
Stored properly at room temperature, the muffins stay fresh for around 2 days. Refrigeration can extend their freshness up to a week.
Can I make these muffins vegan?
Making vegan Pumpkin Cheesecake Muffins requires swapping the eggs, cream cheese, and oil with plant-based alternatives. While possible, it will affect texture and flavor, so adjust accordingly with trusted vegan substitutes.
Final Thoughts
These Pumpkin Cheesecake Muffins are an absolute game changer when you crave a comforting, flavorful baked good that feels both indulgent and wholesome. Once you try them, I know they’ll become your go-to fall treat or anytime pick-me-up. So grab your mixing bowls, pumpkin puree, and cream cheese, and get ready to fill your kitchen with one of the most delightful aromas of the season. Happy baking and even happier eating!
PrintPumpkin Cheesecake Muffins Recipe
These Pumpkin Cheesecake Muffins combine the warm, spiced flavors of pumpkin with a creamy cheesecake center, making a perfect autumn treat for breakfast or dessert. Soft, moist, and bursting with seasonal spices, they are easy to make and sure to impress your family and friends.
- Prep Time: 15 minutes
- Cook Time: 20-25 minutes
- Total Time: 40 minutes
- Yield: 12 muffins 1x
- Category: Breakfast, Dessert, Snack
- Method: Baking
- Cuisine: American
- Diet: Vegetarian
Ingredients
Muffin Batter
- 1 ½ cups all-purpose flour
- 1 cup sugar
- 1 tsp baking powder
- ½ tsp baking soda
- 1 tsp cinnamon
- ½ tsp nutmeg
- ½ tsp salt
- ½ cup vegetable oil
- 2 eggs
- 1 cup pumpkin puree
- 1 tsp vanilla extract
Cheesecake Filling
- 8 oz cream cheese, softened
- ¼ cup sugar
- 1 egg
- 1 tsp vanilla extract
Instructions
- Preheat Your Oven: Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners to prepare for baking.
- Prepare the Muffin Batter: In a medium bowl, whisk together the all-purpose flour, sugar, baking powder, baking soda, cinnamon, nutmeg, and salt. In a large bowl, combine the vegetable oil, eggs, pumpkin puree, and vanilla extract. Gently fold the dry ingredients into the wet mixture until just combined, being careful not to overmix to keep the muffins tender.
- Make the Cheesecake Filling: In another bowl, beat the softened cream cheese, sugar, egg, and vanilla extract together until the mixture is smooth and creamy. This will be the luscious cheesecake center of your muffins.
- Assemble the Muffins: Fill each prepared muffin liner halfway with the pumpkin batter. Add a spoonful of the cheesecake filling on top of the batter, then cover with more pumpkin batter until each liner is about three-quarters full. This layering creates a delightful swirl of flavors and textures.
- Bake to Perfection: Place the muffin tin in the preheated oven and bake for 20-25 minutes, or until a toothpick inserted into the muffin (avoiding the cheesecake center) comes out clean. Remove from the oven, and let the muffins cool in the tin for 5 minutes before transferring them to a wire rack to cool completely.
Notes
- Use canned pumpkin puree or homemade pumpkin puree for best results.
- Make sure the cream cheese is softened to avoid lumps in the cheesecake filling.
- Do not overmix the muffin batter to ensure moist and tender muffins.
- These muffins can be stored in an airtight container in the refrigerator for up to 3 days.
- For a decorative touch, sprinkle a little cinnamon sugar on top before baking.
- Let muffins cool completely before storing to prevent condensation and sogginess.
Nutrition
- Serving Size: 1 muffin
- Calories: 280
- Sugar: 18g
- Sodium: 220mg
- Fat: 15g
- Saturated Fat: 5g
- Unsaturated Fat: 9g
- Trans Fat: 0g
- Carbohydrates: 32g
- Fiber: 2g
- Protein: 4g
- Cholesterol: 55mg
Keywords: pumpkin cheesecake muffins, pumpkin muffins with cream cheese, fall recipes, holiday muffins, autumn baking