Pumpkin Cheesecake Muffins: Moist, Creamy, and Perfect for Fall

Last Updated on August 13, 2025 by Souhail

There’s something magical about that first bite of pumpkin cheesecake muffins, the tender, spiced pumpkin base giving way to a luscious, tangy cream cheese center. Every fall, my kitchen turns into a pumpkin-scented haven, and this recipe is one I keep coming back to year after year.

These muffins are the perfect blend of cozy autumn flavors and creamy indulgence. The pumpkin brings natural sweetness and moisture, while the cheesecake filling adds a dreamy richness that makes them feel like a bakery treat. Whether you enjoy them with your morning coffee, as an afternoon pick-me-up, or as a Thanksgiving dessert, they always hit the spot.

What I love most? They’re incredibly easy to make and taste even better the next day, if you can resist eating them all right away. Trust me, once these beauties hit the cooling rack, you’ll be tempted to grab “just one more” until they mysteriously disappear.

Why These Muffins Are Pure Fall Bliss

If autumn had a signature muffin, this would be it. There’s just the right balance between warm pumpkin spice and creamy cheesecake, making each bite a cozy little moment. Here’s why this recipe works so well:

• Moist and Tender Texture – Pumpkin puree keeps the muffins soft for days.
• Bakery-Style Look – The cheesecake swirl not only tastes amazing but also makes them look professionally made.
• Perfect Flavor Balance – The tangy cream cheese complements the sweet, spiced pumpkin base beautifully.
• Make-Ahead Friendly – They store well, so you can bake them the night before and still have them taste fresh.
• Versatile – Works equally well for breakfast, snacks, or dessert.

Customizing for Your Diet:

• Use gluten-free all-purpose flour for a wheat-free version.
• Swap cream cheese with vegan cream cheese for a dairy-free treat.
• Reduce sugar or use coconut sugar for a less sweet option.

Get Ahead of the Game (So You Can Bake Without Stress)

Let’s be real, baking is a lot more fun when you’re not scrambling around looking for the cinnamon or trying to soften cream cheese at the last second. A little prep makes all the difference:

• Soften the Cream Cheese – Leave it out at room temperature for 30 minutes before you start.
• Measure Your Spices – Pre-measure cinnamon, nutmeg, and any other spices so they’re ready to go.
• Mix Dry Ingredients in Advance – You can combine flour, baking soda, salt, and spices ahead of time.
• Preheat the Oven Early – Muffins love a hot oven from the very start.
• Line or Grease Your Muffin Tin – Saves you time when the batter’s ready to go.

How to Make it

Pumpkin Cheesecake Muffins

Recipe by Souhail

0.0 from 0 votes

Course: Breakfast, BrunchCuisine: AmericanDifficulty: Easy

Servings

12

servings

Prep time

15

minutes

Cooking time

20

minutes

Calories

260

kcal

Soft, spiced pumpkin muffins with a luscious cream cheese center, these bakery-style treats are perfect for cozy mornings or festive gatherings.

Ingredients

• For the Muffin Batter

• 1.75 cups all-purpose flour

• 1 tsp baking soda

• 0.5 tsp salt

• 2 tsp ground cinnamon

• 0.5 tsp ground nutmeg

• 1 cup pumpkin puree (not pumpkin pie filling)

• 1 cup granulated sugar

• 0.5 cup vegetable oil

• 2 large eggs

• 1 tsp vanilla extract

• For the Cheesecake Filling

• 8 oz cream cheese, softened

• 0.5 cup granulated sugar

• 1 large egg yolk

• 0.5 tsp vanilla extract

Directions

• Preheat oven to 350°F. Line a muffin tin with paper liners or lightly grease with cooking spray to prevent sticking.
• In a medium bowl, whisk together flour, baking soda, salt, cinnamon, and nutmeg until the spices are evenly distributed throughout the flour mixture.
• In a separate large bowl, combine pumpkin puree, sugar, oil, eggs, and vanilla until smooth and no streaks remain, making sure the pumpkin and oil are fully incorporated.
• Fold dry ingredients into wet ingredients using a spatula, gently mixing until just combined. Be careful not to overmix, as this can create dense muffins.
• In another bowl, beat cream cheese, sugar, egg yolk, and vanilla until creamy and free of lumps, scraping down the sides of the bowl as needed.
• Fill each muffin liner two-thirds full with pumpkin batter, smoothing the top slightly with the back of a spoon.
• Spoon a generous tablespoon of cheesecake filling over the batter, placing it in the center of each muffin cup.
• Swirl with a toothpick or skewer, making gentle circular motions to create a marbled effect without over-blending the cheesecake into the pumpkin batter.
• Bake for 18–22 minutes, or until the tops are set and a toothpick inserted into the muffin (avoiding the cheesecake center) comes out clean or with just a few moist crumbs.
• Cool in the pan for 5 minutes, then transfer to a wire rack to finish cooling completely before serving.

Notes

• For a stronger spice flavor, add a pinch of ground cloves or allspice.
• Use room-temperature ingredients for a smoother batter and filling.
• Avoid overmixing the batter to keep muffins tender.
• You can double the cheesecake filling for extra creaminess.
• Muffins taste even better the next day once flavors meld.

Nutrition Facts

• Total number of serves: 12
• Calories: 260kcal
• Fat: 13g
• Saturated Fat: 5g
• Cholesterol: 40mg
• Sodium: 220mg
• Carbohydrates: 31g
• Fiber: 1g
• Sugar: 18g
• Protein: 4g

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Pro Tips for Muffin Success

Okay, friend-to-friend, these pumpkin cheesecake muffins are already a star, but there are a few tricks to make sure they come out bakery-perfect every time. I’ve tested these in my own cozy NYC kitchen (while resisting the urge to eat half the batter), and here’s what I’ve learned:

• Room-Temperature Ingredients Are Key – Soft cream cheese blends smoother, and eggs mix better when not ice-cold.
• Don’t Overmix the Batter – Once you combine wet and dry, stop mixing when you no longer see streaks of flour. This keeps muffins tender instead of dense.
• Generous Cheesecake Swirl – Use the full tablespoon for each muffin; it’s the magic bite.
• Check Early for Doneness – Every oven is a little different, so peek at 18 minutes to avoid overbaking.
• Play With Pumpkin Spices – If you love spice-heavy bakes, try adding a pinch of cloves or allspice like I do in my favorite pumpkin muffins recipe.

Variations to Try (Because Why Not?)

One of the best things about this recipe is how adaptable it is. You can swap, twist, and flavor it up to make a new muffin every time.

• Chocolate Chip Pumpkin Cheesecake Muffins – Fold 0.5 cup mini chocolate chips into the pumpkin batter before filling for a sweeter, more decadent version.
• Maple Glazed Muffins – Drizzle with a maple icing after cooling for extra fall flair.
• Nutty Crunch Muffins – Sprinkle chopped pecans or walnuts on top before baking for a crunchy bite.
• Pumpkin Bread Muffin Loaf – Pour the batter into a loaf pan and bake for about 50–55 minutes, similar to my homemade pumpkin bread recipe.
• Cookie-Inspired Muffins – Add a cinnamon-sugar topping for a texture similar to my homemade pumpkin cookies recipe.

Store ’Em, Save ’Em, Love ’Em Later

If you somehow manage to have leftovers (I’m still not sure how that’s possible), here’s how to keep them at their best:

• Room Temperature – Store in an airtight container for up to 2 days.
• Refrigerator – Because of the cream cheese filling, I recommend refrigerating if keeping longer than 2 days. They’ll stay fresh for up to 5 days.
• Freezer – Wrap each muffin in plastic wrap and store in a freezer bag for up to 2 months. Thaw overnight in the fridge before serving.

To reheat, pop them in the microwave for 15–20 seconds or warm in a 300°F oven for 5–7 minutes to bring back that fresh-baked feel.

Creative Uses for These Muffins

If you think muffins are just for breakfast, let me gently prove you wrong. These little pumpkin beauties can pull double (or triple) duty:

• Pumpkin Cheesecake Trifle – Cut muffins into cubes, layer with whipped cream and caramel sauce in a glass.
• Holiday Dessert Board – Arrange them alongside cookies, brownies, and slices of banana pumpkin bread for an autumn-themed platter.
• Pumpkin Sundae Base – Slice in half, top with vanilla ice cream, drizzle with warm caramel, and sprinkle with crushed pecans.

FAQ: Muffin Q&A – Your Questions Answered

Wrapping Up the Muffin Magic

If fall had a signature bake, I’m convinced these pumpkin cheesecake muffins would be it. They’re soft, spiced, and just sweet enough, with that creamy cheesecake center that makes every bite feel like a little celebration. Whether you’re making them for a cozy weekend breakfast, a holiday gathering, or simply to make your kitchen smell like autumn, they’re a guaranteed crowd-pleaser.

So grab your whisk, swirl that cream cheese with confidence, and bake a batch (or two, you’ll thank yourself later). Trust me, once you’ve tried them, this will be the recipe you come back to every pumpkin season.