Name: Pumpkin Cheesecake Muffins with Streusel Topping Recipe
Prep time: 45 min
Cook time: 22 min
Total time: 1 h 7 min
Cuisine: American
Ingredients: 12 ounces full-fat block cream cheese, softened at room temperature; 1 cup powdered sugar; 1 teaspoon vanilla extract; 2/3 cup raw pecan halves; 1/2 cup flour; 1/4 cup packed brown sugar; 1/4 cup granulated sugar; 1/4 teaspoon cinnamon; 6 tablespoons cold butter, cubed (salted or unsalted); 3 eggs; 2 cups granulated sugar; 1 15 oz. can Libby’s pure pumpkin puree (heaping 1 ¾ cup); 1/2 cup vegetable oil; 2 1/2 cups (324 grams) all-purpose flour; 1 1/2 teaspoons baking soda; 1 1/2 teaspoons baking powder; 3/4 teaspoon salt; 3/4 teaspoon ground cinnamon; 3/4 teaspoon ground cloves; 3/4 teaspoon ground nutmeg; 1/2 teaspoon ground ginger; Coarse raw turbinado cane sugar; Ground cinnamon

There’s something about pumpkin and cream cheese that just sings fall to me. These Pumpkin Cheesecake Muffins with Streusel Topping Recipe blend those cozy flavors into the perfect portable treat — moist pumpkin muffin, tangy cream cheese center, and a crunchy pecan streusel all in one bite. You’re going to want to make a double batch!

A close-up view of several muffins stacked on a white plate with a white marbled background. Each muffin has three visible layers: a golden-brown base, a creamy white middle layer, and a crumbly topping. The topping is rough and textured with small nut pieces and sugar crystals, giving a crunchy look. The muffin wrappers are a warm brown color, showing folds and creases. One muffin in the front has its wrapper partially peeled, exposing the creamy middle layer. The lighting highlights the textures and warm tones of the muffins, creating a cozy and inviting feeling. Photo taken with an iphone --ar 2:3 --v 7

Jump to:

Why You'll Love This Recipe
Ingredients & Why They Work
Make It Your Way
Step-by-Step: How I Make Pumpkin Cheesecake Muffins with Streusel Topping Recipe
Top Tip
How to Serve Pumpkin Cheesecake Muffins with Streusel Topping Recipe
Make Ahead and Storage
Frequently Asked Questions:
Final Thoughts
Pumpkin Cheesecake Muffins with Streusel Topping Recipe

Why You'll Love This Recipe

I’ve baked a lot of pumpkin treats over the years, but these Pumpkin Cheesecake Muffins with Streusel Topping Recipe stand out because of their layered textures and balanced sweetness. Plus, the cream cheese filling is such a delicious surprise — like a little creamy treasure inside every muffin.

Layered Flavor Party: The combination of spiced pumpkin with rich cream cheese and crunchy streusel makes every bite exciting.
Perfect for Gifting or Breakfast: These muffins travel well, making them a fantastic homemade gift or a breakfast on-the-go.
Flexible and Friendly: You don’t need fancy ingredients and they’re easy to customize with your favorite spices or nuts.
Impressive Yet Simple: They look like you spent hours baking, but the method is straightforward and beginner-friendly.

The image shows a close-up of a muffin with three visible layers: the bottom and middle layers are a moist, orange-brown cake with a soft texture, the middle has a creamy white filling, and the top layer is a crumbly streusel topping with bits of nuts and sugar crystals giving it a crunchy look. The muffin liner is peeled down around the base, revealing the detailed crumb of the cake. In the background, there are two more muffins slightly out of focus on a white marbled surface. Photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

Each ingredient in this Pumpkin Cheesecake Muffins with Streusel Topping Recipe plays a key role — the pumpkin puree adds moisture and autumn flavor, the cream cheese brings that luscious, tangy sweetness, and the streusel topping provides the perfect crunchy texture contrast. Keep an eye out for fresh spices for maximum flavor!

Flat lay of a block of full-fat cream cheese softened at room temperature on a simple white ceramic plate, a small white ceramic bowl of powdered sugar, a small white ceramic bowl containing vanilla extract, raw pecan halves scattered neatly on a white ceramic dish, a small white ceramic bowl of all-purpose flour, a small white ceramic bowl with packed brown sugar, a small white ceramic bowl of granulated sugar, a small white ceramic bowl with ground cinnamon, cold cubed butter on a white ceramic plate, three whole uncracked brown eggs arranged symmetrically, a small white ceramic bowl of granulated sugar, a small white ceramic bowl filled with bright orange pumpkin puree, a small white ceramic bowl of vegetable oil, a small white ceramic bowl of baking soda with baking powder, a small white ceramic bowl containing ground cloves, ground nutmeg, and ground ginger combined, coarse raw turbinado cane sugar in a small white ceramic bowl, and ground cinnamon sprinkled lightly on the side of a white ceramic plate, all arranged in perfect symmetry and natural proportions, placed on a clean white marble surface, soft natural light, photo taken with an iPhone, professional food photography style, fresh ingredients, white ceramic bowls, no bottles, no duplicates, no utensils, no packaging --ar 2:3 --v 7 --p m7354615311229779997

Cream cheese: Make sure it’s full-fat and softened for smooth mixing and a creamy filling that bakes up perfectly.
Powdered sugar: Blends smoothly into the cream cheese for a silky filling texture.
Raw pecan halves: Adds buttery crunch in the streusel; pulse carefully to avoid overprocessing.
Flour: Use all-purpose and measure correctly (spoon and level or weigh) to keep muffins light, not dense.
Brown and granulated sugar: Provides sweetness and moisture balance in the crumb topping.
Cinnamon and other spices: A warm, cozy spice blend that screams fall in every bite.
Vegetable oil: Keeps muffins moist without overpowering the pumpkin flavor.
Libby’s pumpkin puree: The gold standard for pumpkin flavor and texture — if you use another brand, blot it to remove excess moisture.
Eggs: Bind everything together and add richness.
Baking powder & soda: Help the muffins rise perfectly without collapsing.

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Note: You'll find the complete list of ingredients, along with their exact measurements, in the printable recipe card at the bottom of this post.

Make It Your Way

I love swapping a handful of pecans for walnuts or toasted pumpkin seeds when I want a little twist on this Pumpkin Cheesecake Muffins with Streusel Topping Recipe. Sometimes I even sprinkle a pinch of flaky sea salt on top of the streusel—it’s a game changer!

Nut swaps: Walnuts or toasted seeds work well in the streusel and bring a different crunch and flavor.
Spice tweaks: Add extra ginger or a dash of cardamom for a unique fall spice profile.
Dietary modifications: You can try a dairy-free cream cheese and use coconut oil in place of vegetable oil for a vegan-friendly version.

Step-by-Step: How I Make Pumpkin Cheesecake Muffins with Streusel Topping Recipe

Step 1: Whip Up the Cream Cheese Filling

This part needs a little muscle or a handheld mixer—whisk the softened cream cheese with powdered sugar and vanilla until it’s perfectly smooth. I pop mine in the freezer for about 20-30 minutes while I prep everything else. It firms up nicely but doesn’t freeze solid, so it scoops into nice dollops for the muffins.

Step 2: Make the Streusel Topping

Pulse pecans a few times in your food processor, then add the flour, sugars, and cinnamon. Drop the cold butter cubes on top and pulse until the mix looks like pebble-sized crumbs. If some chunks of butter won't break down, rub them between your fingers to incorporate. Then, keep it in the freezer while you move on—this helps keep the topping crumbly and melt-in-your-mouth once baked.

Step 3: Mix the Wet and Dry Ingredients Separately

In one big bowl, gently whisk the eggs, mix in the sugar, pumpkin puree, and oil. In another, combine the flour, baking soda, baking powder, salt, and all the warming spices like cinnamon, cloves, nutmeg, and ginger. Keeping these separate until the next step helps avoid overmixing.

Step 4: Combine the Batter

Pour the dry ingredients into the wet and stir just until combined—don’t overmix or your muffins could get tough. The batter should be thick but spreadable, like autumn in a bowl.

Step 5: Assemble the Muffins

Use a cookie scoop to drop about 1.5 tablespoons of batter into each muffin liner, spreading it to cover the bottom nicely. Add a rounded tablespoon of the cream cheese filling next, then top with the remaining batter. Finally, heap a generous tablespoon of streusel on each and gently press it down so it bakes in place instead of falling off later.

Step 6: Bake and Cool

Bake at 350°F for 20-22 minutes, testing doneness with a toothpick inserted into the batter (try not to touch the cream cheese center). Softer cream cheese filling means longer bake time, so keep an eye near the 22-minute mark. Let muffins cool for 5 minutes before transferring to a wire rack. I like to sprinkle some ground cinnamon and coarse turbinado sugar on top once cooled for a little extra sparkle and crunch.

Top Tip

Making these Pumpkin Cheesecake Muffins with Streusel Topping Recipe a few times taught me that handling the cream cheese filling temperature is key. Chill it enough so it holds its shape but isn’t rock hard. Plus, measuring flour by weight drastically improves your muffin’s texture—do not underestimate this!

Cream Cheese Chill Time: Freeze the filling for 20-30 minutes before scooping, so it stays intact but is still pliable to handle.
Flour Measurement: Fluff, spoon, and level your flour if you don’t weigh it, avoiding dense muffins.
Streusel Texture: Keep the butter cold and pulse just enough—you want little pebbles, not a paste.
Baking Time Watch: Start checking at 20 minutes if your cream cheese is soft; longer if chilled harder—but always test with a toothpick away from the cream cheese.

How to Serve Pumpkin Cheesecake Muffins with Streusel Topping Recipe

pumpkin cheesecake muffins - Serving Suggestion

Garnishes

I love dusting the tops with a little ground cinnamon and coarse turbinado sugar right after baking—it adds a subtle crunch and a classic fall aroma. Sometimes, a tiny drizzle of maple syrup finishes them off beautifully if I’m serving for brunch.

Side Dishes

These muffins pair wonderfully with a warm cup of spiced chai or your favorite coffee. For a heartier breakfast, add a side of scrambled eggs or a fresh fruit salad to balance out the richness.

Creative Ways to Present

For holiday gatherings, I like to arrange these Pumpkin Cheesecake Muffins with Streusel Topping Recipe on a rustic wooden board surrounded by autumn leaves and cinnamon sticks. Wrapping them individually in parchment tied with twine makes a charming edible gift that's sure to impress.

Make Ahead and Storage

Storing Leftovers

I store leftover muffins in an airtight container in the fridge after letting them come to room temperature for a couple hours. Placing parchment between layers prevents them from sticking. They stay fresh and soft for about 3–5 days this way.

Freezing

These muffins freeze beautifully! Just wrap each individually in plastic wrap and pop in a freezer-safe bag. When you want a treat, thaw at room temp or warm briefly in the microwave. The cream cheese filling stays creamy without getting icy.

Reheating

I heat mine in the microwave for about 15 seconds to bring out that fresh-baked softness, especially if refrigerated or frozen. This little burst of warmth makes the cream cheese filling extra melty and the streusel pleasantly crisp again.

Frequently Asked Questions:

Can I substitute low-fat cream cheese in the Pumpkin Cheesecake Muffins with Streusel Topping Recipe?

Using low-fat cream cheese might affect the texture and richness of the filling, potentially making it less smooth and flavorful. For the best results, stick with full-fat cream cheese as noted in the recipe.

How do I prevent the streusel topping from falling off the muffins?

Make sure to gently press the streusel topping into the batter before baking. This small step helps it adhere better during baking, so it stays put and gives you that delightful crunchy top.

Can I prepare the batter ahead of time?

You can prep the batter and fillings a few hours in advance. Keep the cream cheese filling and streusel topping refrigerated separately until you assemble and bake to ensure the best texture and rise.

What’s the best way to measure flour for this recipe?

For accuracy, weigh your flour if you have a kitchen scale. If not, fluff the flour, spoon it lightly into your measuring cup, and level it off with a knife rather than scooping directly from the bag to avoid compacting and dense muffins.

Final Thoughts

This Pumpkin Cheesecake Muffins with Streusel Topping Recipe has become one of my go-to fall treats. The way the cream cheese center stays soft and creamy inside the spiced pumpkin muffin, plus that crunchy topping, just makes me smile every time. I hope you find as much joy baking and sharing these as I do. Trust me, once they’re out of the oven, you won’t want to eat just one!