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; 1½ teaspoons baking soda; 1½ 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 so cozy about these Pumpkin Cheesecake Muffins with Streusel Topping Recipe—they combine the rich creaminess of cheesecake with the spice-packed warmth of pumpkin and a crunchy, buttery streusel that just makes your kitchen smell like fall happiness. Trust me, making these is totally worth the little bit of extra effort!

The image shows a close-up of several muffins stacked in a pile on a white plate. Each muffin has three visible layers: the bottom layer is golden brown and moist, the middle layer is creamy white filling inside one muffin with its baking liner peeled back, and the top layer is a crumbly, textured coating of light brown streusel with visible small nut pieces and sugar crystals scattered on top. The muffins are in brown paper liners with the plate set on a white marbled surface. The lighting highlights the crumbly texture and creamy filling in sharp detail. 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 love sharing this Pumpkin Cheesecake Muffins with Streusel Topping Recipe because it’s one of those treats that feels special enough for a holiday brunch but simple enough for a regular weekend at home. The layers of flavor—from a luscious cream cheese center to a perfectly spiced pumpkin base—make every bite memorable.

Perfect Balance: The cream cheese filling offers a silky contrast to the spiced pumpkin muffin, making each bite both rich and light.
Crunchy Streusel Topping: That buttery streusel with pecans adds delightful texture and an irresistible nutty crunch.
Feeds a Crowd: This recipe makes 22 muffins—great for sharing or for a week’s worth of breakfasts or snacks.
Seasonal Flavor Bomb: The warming spices like cinnamon, cloves, and nutmeg evoke cozy fall vibes without being overpowering.

A close-up of a muffin with three visible layers: the bottom layer is a moist brown cake with a soft texture, the middle layer is a creamy white filling that looks smooth and thick, and the top layer is a crumbly streusel topping made of small brown and tan crumbs with bits of nuts scattered. The muffin liner is pulled down, showing the inside of the muffin. Other muffins with similar layers are blurred in the background, all placed on a white marbled surface. Photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

The magic of this Pumpkin Cheesecake Muffins with Streusel Topping Recipe lies in the harmony between the creamy, spiced, and crunchy components. Each ingredient plays a role in creating that perfect bite, and choosing fresh spices and quality cream cheese will really elevate your outcome.

Flat lay of a block of soft full-fat cream cheese, a small white bowl of powdered sugar, a small white bowl of vanilla extract, raw pecan halves, a small white bowl of all-purpose flour, packed brown sugar crystals in a small white bowl, granulated sugar in a small white bowl, ground cinnamon in a small white bowl, cold cubed butter, three whole uncracked brown eggs, granulated sugar in a larger white bowl, bright orange pumpkin puree in a small white bowl, a small white bowl of vegetable oil, all-purpose flour, baking powder and baking soda mixed with ground cinnamon, ground cloves, ground nutmeg, ground ginger and salt in a white bowl, coarse raw turbinado cane sugar crystals in a small white bowl, and ground cinnamon in another small white bowl, all arranged symmetrically in a clean, natural and fresh state on simple white ceramic bowls, 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: It’s essential for that smooth, rich cheesecake center—avoid low-fat versions since they won’t set properly.
Powdered sugar: Dissolves easily in the cream cheese for a silky filling without grit.
Raw pecan halves: Give your streusel that lovely nutty crunch; lightly pulsing them keeps pieces visible and satisfying.
Flour: All-purpose flour provides structure; remember to measure carefully or weigh it for the best texture.
Brown and granulated sugar: The brown sugar adds moisture and depth to the streusel, while granulated sugar gives sweetness and a little snap.
Cinnamon, cloves, nutmeg, ginger: These warming spices make the muffins truly seasonal—freshly ground is best if you have it.
Vegetable oil: Keeps muffins moist without altering flavor.
Libby’s pure pumpkin puree: Known for consistent texture and flavor, but if you use a different brand, blot excess moisture for best results.
Eggs: Bind everything together and add richness.
Baking powder and baking soda: Help the muffins rise beautifully so they’re soft and fluffy.
Cold butter: Key to creating those perfect crumbly streusel bits.

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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 like to tailor this recipe based on what I have at hand or the occasion. Sometimes I swap pecans for walnuts or add a pinch of cardamom for an extra layer of spice. Feel free to experiment—it’s the kind of recipe that invites little tweaks!

Variation: Once, I swapped the streusel topping for a simple cinnamon sugar blend, which made for a lighter crunch when I was short on butter and nuts—still delicious and a bit quicker.
Dietary Changes: To make these dairy-free, you can try a vegan cream cheese and coconut oil in the streusel, though the texture and flavor will shift slightly.
Spice Level: Adjust the spice amounts to suit your taste—less clove and nutmeg will give you a milder pumpkin flavor perfect for picky eaters.

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

Step 1: Prep the Cream Cheese Filling

Start by softening the cream cheese until it’s room temperature—it’s much easier to whisk smooth without lumps. Add in the powdered sugar and vanilla, then whisk vigorously by hand or use a handheld mixer. I usually freeze this for about 20-30 minutes while I prepare the batter so it firms up just enough to scoop yet stays pliable.

Step 2: Make the Streusel Topping

Pulse the pecans a few times in a food processor, just until chopped but not ground into dust. Add the flour, sugars, and cinnamon, then pulse a few more times to combine. Sprinkle in cubed cold butter and pulse again until the mixture looks like small, coarse crumbs. If you don’t have a food processor, I’ve found cutting in the butter by hand works perfectly fine too.

Step 3: Prepare Your Muffin Tins and Batter

Preheat your oven to 350°F and line two muffin tins with 22 liners. Give them a quick spray with nonstick spray to make sure the muffins release easily. In one bowl, whisk your eggs gently, then stir in sugar, pumpkin puree, and oil. In another bowl, whisk together the flour, baking powder, soda, salt, and spices for even distribution.

Step 4: Combine and Layer

Gently fold the dry ingredients into the wet until just moistened—overmixing can make muffins tough. Use a cookie scoop or tablespoon to spoon about 1½ tablespoons of pumpkin batter into each liner and spread evenly. Add a rounded tablespoon of the cream cheese filling atop that, then cover with more pumpkin batter. Finally, top each muffin with a generous scoop of streusel crumb and gently press it in so it sticks while baking.

Step 5: Bake and Cool

Bake for 20-22 minutes, but keep an eye on them—the baking time can fluctuate based on how chilled your cream cheese filling is. The best way to check doneness is by inserting a toothpick into the top batter part without touching the cream cheese; it should come out clean. Let the muffins cool for about 5 minutes before transferring them to a wire rack to cool completely or just slightly warm.

Top Tip

After making these muffins many times, I’ve learned a few key tricks that really help them turn out perfectly every time. These tips will save you from common pitfalls and keep you baking like a pro!

Correct Cream Cheese Temperature: Leaving the cream cheese too soft makes the filling too runny—it won’t hold its shape when baking, so aim for stiff but scoopable.
Measure Flour Properly: Too much flour makes denser muffins, so fluff then spoon and level it instead of scooping for the best texture.
Keep Butter Cold for Streusel: This helps create those lovely pebble-like crumbs instead of a melted mess.
Watch Baking Time: Since the cream cheese affects moisture, check muffins near 20 minutes instead of following the clock rigidly to avoid overbaking.

How to Serve Pumpkin Cheesecake Muffins with Streusel Topping Recipe

Pumpkin Cheesecake Muffins - Serving Suggestion

Garnishes

I usually sprinkle a pinch of coarse raw turbinado cane sugar and a dash of cinnamon on top right out of the oven. It adds a little sparkle and an extra crunch layer I adore. Sometimes a light dusting of powdered sugar works beautifully too, especially if you’re serving them for breakfast or brunch guests.

Side Dishes

These muffins pair wonderfully with a hot cup of coffee, chai tea, or even a creamy latte. I also like serving them alongside scrambled eggs or a fruit salad to balance the richness during a brunch spread.

Creative Ways to Present

For a cozy fall gathering, I’ve lined a rustic wooden tray with a plaid cloth and arranged the muffins with mini pumpkins and cinnamon sticks scattered around. Wrapping a few muffins individually in parchment tied with twine is perfect for gifting. You can also serve them warm with a dollop of whipped cream or vanilla yogurt on the side for a little indulgence.

Make Ahead and Storage

Storing Leftovers

I let these muffins cool completely before storing them in an airtight container in the fridge. If you’re stacking, I place parchment sheets between layers to keep the streusel topping intact. They stay fresh for up to 5 days, but honestly, they never last that long in my house!

Freezing

To freeze, wrap muffins individually in plastic wrap then place them in a freezer-safe bag or container. When you want one, just thaw at room temperature or gently warm in the microwave for 15-20 seconds. I’ve found this keeps their texture and flavor surprisingly well.

Reheating

The best way I’ve found to reheat these muffins is either a quick zap in the microwave for about 10 seconds to soften the cream cheese center or a few minutes in a 300°F oven to bring back that fresh-baked texture. Just be careful not to overheat, or the cream cheese can become too soft.

Frequently Asked Questions:

Can I use canned pumpkin pie filling instead of pumpkin puree?

Canned pumpkin pie filling has added sugars and spices which might throw off the balance of flavors and sweetness in this recipe. It’s best to use pure pumpkin puree and add your own spices for control and the best texture.

How do I know when the muffins are fully baked?

Insert a toothpick into the pumpkin batter part of the muffin, avoiding the cream cheese layer. If it comes out clean or with just a few crumbs, the muffins are done. Also, look for golden streusel and slightly pulling away edges.

Can I make these muffins dairy-free?

Yes! Substituting cream cheese with a dairy-free alternative and using a plant-based butter or coconut oil in the streusel works well, though the texture will be slightly different. Using full-fat dairy-free cream cheese is key to getting that luscious filling.

Why is it important to freeze the cream cheese filling before assembling?

Freezing the cream cheese mixture firms it up so you can easily scoop and layer it between the pumpkin batter. If it’s too soft, the cream cheese might blend into the batter while baking rather than creating the distinct creamy center that makes these muffins special.

Final Thoughts

Honestly, these Pumpkin Cheesecake Muffins with Streusel Topping Recipe have become a fall staple in my kitchen because they offer such a delightful mix of textures and flavors that feel both indulgent and comforting. Whether you’re feeding family, bringing treats to work, or just baking for yourself, I’m confident these muffins will brighten your day and become a favorite tradition. Give them a try—you won’t regret it!