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 magical about biting into a soft, spiced muffin filled with creamy cheesecake and topped with a crunchy streusel. This Pumpkin Cheesecake Muffins with Streusel Topping Recipe is exactly that kind of treat—comfort food wrapped up in a perfectly portable form. You’ll want to make these for breakfast, brunch, or really any time you need a little cozy pick-me-up.

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 remember the first time I tried these muffins—they immediately felt like a warm hug on a chilly morning. What’s not to love about the tender pumpkin muffin base married with tangy cream cheese filling, finished off with a buttery, nutty streusel? Trust me, these become instant favorites in any household.

Perfect Balance of Textures: The creamy filling contrasts beautifully with the soft muffin and crunchy streusel topping.
Ideal Fall Flavor: Pumpkin, cinnamon, nutmeg, and cloves make each bite scream cozy autumn vibes.
Great for Make-Ahead: You can prep the filling and streusel ahead, making morning baking a breeze.
Family Friendly: Kids love these muffins almost as much as adults, and they’re perfect for sharing.

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

Every ingredient in these Pumpkin Cheesecake Muffins with Streusel Topping Recipe serves a purpose, working harmoniously to deliver texture, flavor, and that classic fall warmth we all crave. Here are a few tidbits on each to help you shop smart and bake like a pro.

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

Full-fat block cream cheese: Gives the filling its creamy richness; block form whips up better than the spreadable kind.
Powdered sugar: Keeps the cheesecake filling silky smooth without any grittiness.
Vanilla extract: Adds warmth and depth to the cream cheese aroma.
Raw pecan halves: Chopped for a buttery crunch in the streusel topping that bursts with nutty flavor.
Flour: Binds the muffin batter and streusel; measuring correctly (fluff, spoon, level!) helps keep muffins tender, not dense.
Brown and granulated sugars: Sweeten and add moisture; brown sugar lends some caramel notes to the topping.
Cinnamon, ground cloves, nutmeg & ginger: Classic pumpkin spice combo that makes your kitchen smell amazing while baking.
Cold butter: Essential for that crumbly, pebble-like streusel texture.
Eggs: Bind everything together and provide structure to the muffins.
Libby’s pure pumpkin puree: The gold standard for pumpkin baking—just make sure to drain excess moisture if using another brand.
Vegetable oil: Keeps muffins moist without weighing them down.

📝

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 like to jazz this recipe up depending on the season or my mood. You can easily swap pecans for walnuts or even pumpkin seeds if you want a change in streusel crunch. Sometimes I sprinkle a little coarse raw sugar on top for extra sparkle.

Variation: I’ve tried swapping half the all-purpose flour for whole wheat flour to add nuttiness and fiber. The muffins turn out a bit heartier but still delicious! Just be sure not to overmix.

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

Step 1: Cream Cheese Filling Prep

Combine full-fat cream cheese, powdered sugar, and vanilla in a bowl. Whisk it until perfectly smooth—this requires a bit of elbow grease, or use a handheld mixer if you’d rather save your wrists. Once it’s silky and lump-free, pop it in the freezer for about 20 to 30 minutes. It should be firm but still scoopable—this step helps the cheesecake layer hold its shape inside the muffin.

Step 2: Make the Streusel Topping

Pulse raw pecans a few times in the food processor so they’re chopped but not pulverized. Add the flour, brown sugar, granulated sugar, and cinnamon and give it a few more pulses. Finally, drop in the cold cubed butter and pulse until the mix looks like little pebbles. If there are stubborn chunks of butter, rub them between your fingers to break up. You want those tiny butter pockets that melt during baking to give the topping that classic crumble texture. Freeze the streusel while prepping the batter.

Step 3: Prep Your Muffin Tins and Oven

Preheat your oven to 350°F. Line two muffin tins with 22 liners total, then lightly spray with nonstick cooking spray. This makes cleanup easier and helps the muffins release beautifully.

Step 4: Mix Wet Ingredients

In a large bowl, whisk the eggs gently until combined. Stir in the granulated sugar, pumpkin puree, and vegetable oil. The batter will look shiny and smooth — it’s smelling like fall already!

Step 5: Mix Dry Ingredients

In a separate bowl, whisk together the all-purpose flour, baking powder, baking soda, salt, cinnamon, cloves, nutmeg, and ginger until well combined.

Step 6: Combine Wet & Dry

Slowly add the flour mixture to the pumpkin mixture, stirring just until everything is combined. Don’t overmix here or your muffins might turn out tough — a few lumps are perfectly fine.

Step 7: Assemble Muffins

Using a cookie scoop or spoon, drop 1 ½ tablespoons of the pumpkin batter into each muffin liner and spread it to cover the bottom. Next, add 1 rounded tablespoon of the cream cheese filling on top of the batter—you want to get a nice layer without it spilling over. Cover the cream cheese with the remaining pumpkin batter, dividing it evenly among the cups. Finally, sprinkle a heaping tablespoon of the chilled streusel over the top and gently pat it down so it adheres during baking.

Step 8: Bake to Perfection

Bake at 350°F for 20 to 22 minutes, or until a toothpick inserted into the muffin top (avoiding the cream cheese) comes out clean. Keep in mind that if your cream cheese filling is softer, it might take a few extra minutes. Don't open the oven too early — those muffins need their time to rise and bake through perfectly.

Step 9: Cool and Garnish

Let the muffins cool in the tin for 5 minutes, then move them to a wire rack. For a pretty touch, sprinkle with a dash of ground cinnamon and some coarse raw turbinado sugar. I love serving these warm, but they’re just as good at room temperature or lightly microwaved for 10 seconds if you want that fresh-baked vibe.

Top Tip

After testing this recipe many times, I discovered a few key tricks that really make your Pumpkin Cheesecake Muffins with Streusel Topping Recipe come out bakery-worthy every time.

Cream Cheese Texture Matters: Make sure the cream cheese filling is cold but scoopable — too soft and it will melt away, too hard and it won’t create that perfect pocket inside the muffin.
Measure Flour Carefully: Using a kitchen scale or fluffing and spooning the flour prevents dense muffins.
Don’t Overmix: Combine just until the batter comes together. Overmixing creates tough muffins instead of tender ones.
Pat Streusel onto Batter: Gently pressing the streusel helps it stick so you get that gorgeous crunchy topping instead of it falling off after baking.

How to Serve Pumpkin Cheesecake Muffins with Streusel Topping Recipe

Pumpkin Cheesecake Muffins - Serving Suggestion

Garnishes

I love a light dusting of cinnamon sugar on top just before serving—it adds shimmer and a little crunchy sweetness. Sometimes a tiny dollop of whipped cream or a drizzle of maple syrup feels just right, especially on extra chilly mornings.

Side Dishes

These muffins pair beautifully with a hot cup of coffee or spiced chai tea. For brunch, I often serve them alongside fresh fruit or a dollop of yogurt to balance the richness.

Creative Ways to Present

Hosting a fall gathering? Place the muffins on a tiered stand, with little flags or seasonal leaves tucked around the tiers for a festive touch. Or, line a basket with a cozy linen napkin and arrange them alongside mini jars of honey or housemade butter to make guests feel extra special.

Make Ahead and Storage

Storing Leftovers

I usually let leftover muffins cool completely before placing them in an airtight container. They stay fresh at room temperature up to 2 hours and then longer in the fridge—perfect for a grab-and-go breakfast during busy mornings.

Freezing

These muffins freeze exceptionally well. I wrap each one tightly in plastic wrap, then store them in a freezer-safe zip bag. When I want to enjoy one, I thaw at room temp or toss it in the microwave for 15-20 seconds—still moist and delicious!

Reheating

To get that fresh-out-of-the-oven warmth, I microwave a muffin for 10-15 seconds or pop it in a 325°F oven for 5 minutes. Just be cautious not to overheat the cream cheese center or it might get a little runny.

Frequently Asked Questions:

Can I use canned pumpkin pie mix instead of pure pumpkin puree?

You shouldn’t substitute canned pumpkin pie mix here, as it contains added sugars and spices. Using pure pumpkin puree ensures you control the flavor balance and don’t end up with overly sweet or spiced muffins.

How do I prevent the cream cheese from leaking out during baking?

Make sure your cream cheese filling is firm but scoopable when assembling. Freezing the filling for 20-30 minutes before use helps it hold shape inside the muffin. Also, gently patting the streusel topping down over the batter holds everything in place better.

Can I make these muffins gluten-free?

Yes, you can swap the all-purpose flour with a gluten-free flour blend that measures cup-for-cup. Just check that your blend contains xanthan gum or add a bit if necessary to maintain structure. Baking time may vary slightly so keep an eye on them.

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

For the best texture, weigh your flour using a kitchen scale. If you don’t have one, fluff the flour in the container, spoon it into your measuring cup, and level it off with a knife. Avoid scooping directly with the cup as this compacts the flour and can make your muffins dense.

Final Thoughts

This Pumpkin Cheesecake Muffins with Streusel Topping Recipe is one of those gems I come back to year after year. It’s easy to make, perfectly balanced, and fills your kitchen with the best aromas. Whenever I bake a batch, I end up sneaking more than my fair share—so I hope you love it as much as I do and add it to your seasonal baking repertoire. Trust me, your friends and family will be asking for it on repeat!