Autumn mornings have a way of sneaking into your senses—the crispness in the air, the golden leaves drifting lazily to the ground, and the irresistible scent of spices that instantly makes everything feel cozy.
Now, imagine that very feeling, not in a bustling bakery, but right in your own kitchen. That’s exactly what happens when you bake these Pumpkin Muffins with Cream Cheese Filling.
From the moment you start mixing, the magic begins. The rich pumpkin batter, infused with cinnamon, nutmeg, and a touch of pumpkin pie spice, fills the air with the warm, comforting aroma of fall. It’s the kind of scent that makes you pause, take a deep breath, and smile.
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And just when you think it couldn’t get any better, there’s the cream cheese filling—a silky, sweet surprise tucked inside each muffin.
But that’s not all. A buttery, cinnamon-sugar crumb topping crowns each muffin, adding a gentle crunch that contrasts beautifully with the soft, tender pumpkin cake and creamy center.
Every layer—moist pumpkin, smooth cheesecake, and crisp crumble—works together like a symphony of flavors and textures. Some bites will give you a peek of cream cheese peeking through the top or sides, teasing you before you even take your first bite.
If I had to pick just one baked good to make over and over again during autumn, it would be these muffins. They’re not just muffins; they’re an experience.
The moist pumpkin base brings all the cozy spice notes of the season, while the rich cream cheese center is like discovering a hidden pocket of cheesecake in every bite.
Then there’s the crumb topping—sweet, buttery, and slightly crunchy—that makes each muffin taste like a cross between pumpkin coffee cake and pumpkin swirl cheesecake. Every layer adds something special, and together they create the perfect fall treat.
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These muffins aren’t just dessert—they’re breakfast, snack, and treat all in one. They travel well for lunchboxes, delight friends and family, and even freeze beautifully so you can enjoy a taste of fall anytime.
Each muffin is a little celebration of the season, from the spiced batter to the creamy filling and crumbly topping.
Whether you’re sipping a cup of coffee on a chilly morning, serving them at a brunch, or simply sneaking one straight from the oven, these muffins have a way of making any moment feel cozy and indulgent.
They’re better than bakery muffins, easier to make than you’d think, and perfectly designed to capture the very essence of fall in every bite.
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So grab your mixing bowls, your pumpkin purée, and that cream cheese hiding in the fridge. It’s time to bring the bakery magic home and make these Pumpkin Cream Cheese Muffins the centerpiece of your autumn mornings. Trust me—once you take a bite, you’ll understand why these are a seasonal favorite.
So if “make cream cheese–stuffed pumpkin muffins” isn’t already on your fall to-do list, it’s time to add it. These muffins are everything you love about the season—warm, cozy, sweet, and spiced—wrapped up in one bakery-style treat that you’ll want to make again and again.
You might also love these cozy fall favorites: Banana Bread Recipe & Pumpkin Spiced Bread Recipe - perfect companions to your autumn baking lineup!
You might also love these cozy fall favorites, pumpkin everything muffin recipes:
INGREDIENTS
Pumpkin Muffins
- 1 and 3/4 cups (219g) all-purpose flour (spooned & leveled)
- 1 teaspoon store-bought or homemade pumpkin pie spice
- 1/2 cup (100g) packed light or dark brown sugar
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- 2 teaspoons ground cinnamon
- 1/2 cup (100g) granulated sugar
- 2 large eggs, at room temperature
- 1 cup (227g) canned pumpkin puree
- 1/2 cup (120ml) vegetable oil (or melted coconut oil)
- 1/3 cup (80ml) milk
- 1/2 teaspoon salt
- 1 teaspoon pure vanilla extract
Cream Cheese Filling
- 6 ounces (170g) full-fat brick cream cheese, softened to room temperature
- 1 egg yolk, at room temperature
- 1/2 teaspoon pure vanilla extract
- 3 Tablespoons (36g) granulated sugar
Crumb Topping
- 1/3 cup (67g) packed light or dark brown sugar
- 1 teaspoon ground cinnamon
- 1/4 cup (4 Tbsp; 56g) unsalted butter, melted
- 2/3 cup (84g) all-purpose flour
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RECIPE INSTRUCTIONS
#1 Preheat the oven to 425°F (218°C). Grease a 12-cup muffin tin with nonstick spray or line it with cupcake liners. Since this recipe yields about 12–14 muffins, you might need a second pan or bake in two batches.
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#2 Start with the crumb topping: In a small bowl, stir together the brown sugar, cinnamon, and melted butter until well blended. Add the flour and lightly mix with a fork until crumbly. Avoid over-mixing into a paste—stop once crumbs form. Set aside.
#3 Prepare the pumpkin batter: In a large bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, and pumpkin pie spice. Set aside. In a separate medium bowl, combine the brown sugar, granulated sugar, eggs, pumpkin puree, oil, milk, and vanilla, whisking until smooth. Gently pour the wet mixture into the dry ingredients and stir or whisk only until just blended—do not over-mix.
#4 Prepare the cheesecake filling: With a handheld or stand mixer fitted with a paddle or whisk attachment, beat the cream cheese in a medium bowl on medium-high speed until soft and creamy. Add the egg yolk, vanilla extract, and sugar, then continue mixing until fully combined.
#5 Spoon a heaping tablespoon of pumpkin batter into each muffin cup. Add about a spoonful (just under a full tablespoon) of cheese filling on top, then cover with another heaping tablespoon of batter—or enough to fill each cup to the top. It’s fine if some cheesecake filling peeks through the top or sides.
#6 Finish by sprinkling the crumb topping over each muffin, gently pressing it down so it sticks during baking.
#7 If you want swirl pumpkin cream cheese muffins, then don't add crumb topping. Just top each muffin with about 1 tablespoon of cream cheese mixture and use a toothpick to swirl it into the batter. This will not look smooth, but it will bake up much prettier.
#8 Optional Topping: Before baking, sprinkle your muffins with chopped almonds, walnuts, or your favorite nuts, and add a little sugar on top for extra crunch and sweetness. This gives your pumpkin muffins a delightful texture and a beautiful, golden finish.
#9 Bake at 425°F (218°C) for 5 minutes, then—without removing the muffins—lower the oven temperature to 350°F (177°C) and bake for an additional 15–17 minutes. The total bake time should be about 20–22 minutes. Let the muffins cool in the pan for at least 10 minutes before serving.
#10 Store any leftover muffins in an airtight container—keep them at room temperature for up to 2 days, or refrigerate for up to 1 week.
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If you love this, you’ll definitely want to try this Peach Cobbler Recipe. Keep the cozy going with this seasonal must-try!
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