Name: Pumpkin Cheesecake Muffins with Streusel 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 utterly comforting about these Pumpkin Cheesecake Muffins with Streusel Recipe. Imagine tender pumpkin muffins with a creamy cheesecake center and a crunchy pecan streusel topping—each bite feels like a perfect fall hug. They’re worth every minute to make, trust me!

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 Recipe
Top Tip
How to Serve Pumpkin Cheesecake Muffins with Streusel Recipe
Make Ahead and Storage
Frequently Asked Questions:
Final Thoughts
Pumpkin Cheesecake Muffins with Streusel Recipe

Why You'll Love This Recipe

This recipe has quickly become one of my favorites for so many reasons. It’s the perfect balance of flavors and textures, and it’s surprisingly straightforward to pull off even on a busy day when you want something delicious and a little special.

Perfect texture combination: Soft pumpkin muffins meet rich, creamy cheesecake with a crunchy pecan streusel on top.
Make-ahead convenience: You can prep the cream cheese filling and streusel early to save time on the day you bake.
Seasonal flavors you’ll adore: Warm spices like cinnamon, nutmeg, and cloves mix beautifully with real pumpkin puree.
Fun and foolproof assembly: Layering the batter, cheesecake, and streusel is easier than it looks, even if you’re not a pro baker.

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

There’s a reason these ingredients come together so well. The cream cheese adds that luscious, velvety filling that contrasts perfectly with the moist pumpkin muffin, while the pecan streusel topping delivers a nutty crunch. Here are some tips to keep in mind when gathering your ingredients.

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: Go for full-fat and softened—but not melted—to get that rich, creamy filling texture that stays intact after baking.
Powdered sugar: Smooth and fine, it blends seamlessly into the cream cheese for the filling.
Vanilla extract: Just a touch brightens the flavor beautifully without overpowering the pumpkin.
Raw pecan halves: Pulse them coarsely in the food processor for that perfectly crumbly streusel texture.
Flour: I recommend weighing it if you can, or fluff and spoon it lightly to keep your muffins from turning dense.
Brown and granulated sugar: Together they give the streusel that deep caramel sweetness and a bit of crunch.
Pumpkin puree: Libby’s is my go-to for consistent flavor and moisture, but if you use another brand, blot it to avoid extra liquid in the batter.
Spices (cinnamon, cloves, nutmeg, ginger): These create the cozy fall flavor profile that makes pumpkin muffins so special.
Vegetable oil: Keeps the muffins moist and tender without adding flavor, letting the pumpkin and spices shine.

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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

One of the best parts about this Pumpkin Cheesecake Muffins with Streusel Recipe is how adaptable it is. I love tweaking the streusel or spices depending on what I have on hand or the mood I’m in.

Variation: Adding chopped crystallized ginger to the streusel gives a surprising zesty kick that I found delightful. It balances the sweetness beautifully.
Dairy-free option: I’ve tried substituting vegan cream cheese and butter in the streusel, and while the texture is slightly different, it still makes a fantastic treat for dairy-free friends.
Less sweet: If you prefer milder sweetness, simply reduce the sugar in the pumpkin batter by ¼ cup without sacrificing moisture or flavor.
Mini muffins: Perfect for parties! Just shorten baking time by about 8 minutes and keep a close eye—they bake quickly.

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

Step 1: Preparing the Cream Cheese Filling

Start by softening your full-fat cream cheese at room temperature. Then whisk it along with powdered sugar and vanilla extract until silky smooth. It’s a bit of a workout if you're whisking by hand—so don’t be shy to use a handheld mixer if you’ve got one handy. Pop this mixture in the freezer while you work on your batter; you want it firm but still scoopable. This step is crucial to achieve that dreamy cheesecake center that doesn’t melt away too much during baking.

Step 2: Making the Pecan Streusel Topping

For that irresistible crunchy topping, pulse pecan halves in a food processor just a few times — you don’t want them completely chopped. Then add your flour, brown sugar, granulated sugar, and cinnamon and pulse a few more times to mix. Next, scatter your cold, cubed butter on top and give it a few final pulses until the mixture resembles tiny pebbles. If bits of butter are still too large, rub them between your fingers to work them into the streusel. Quick tip: keeping the streusel cold ensures a beautiful crumbly texture after baking. Freeze it while you prep the rest.

Step 3: Mixing Wet and Dry Ingredients Separately

Preheat your oven to 350°F and get your muffin pans ready with liners and a light spray of nonstick spray — this helps with easy muffin release. In a large bowl, gently whisk together the eggs first, then add sugar, pumpkin puree, and vegetable oil until combined but not over-whipped. In a separate bowl, whisk together your flour, baking powder, baking soda, salt, and a blend of spices (cinnamon, cloves, nutmeg, and ginger) ensuring they’re evenly distributed for consistent flavor.

Step 4: Combining Batters and Assembling Muffins

Fold the dry ingredients into your pumpkin mixture just until everything is incorporated—don’t overmix, or your muffins might turn out tough. Now for the fun part! Use a cookie scoop to spoon about 1½ tablespoons of pumpkin batter into each muffin liner, spreading it gently to cover the bottom. Next, add a rounded tablespoon of cream cheese filling on top of the batter. Cover the cheesecake dollop with the remaining pumpkin batter, then top each cup generously with your chilled streusel, patting it down lightly so it sticks. This layer is what seals in all the delicious textures.

Step 5: Baking and Cooling

Bake for 20 to 22 minutes at 350°F, but keep in mind baking time depends on how soft or firm your cream cheese filling is. A slightly softer filling can mean a longer bake. To test, insert a toothpick into the top (avoiding the cream cheese) — it should come out clean. Cool the muffins for five minutes before moving them to a wire rack. If you want to add a little extra something, sprinkle with ground cinnamon and turbinado cane sugar right after baking. Enjoy these warm or at room temperature; a quick zap in the microwave revives their fresh-baked goodness.

Top Tip

From my experience making Pumpkin Cheesecake Muffins with Streusel Recipe multiple times, a few small tweaks make all the difference between good and absolutely show-stopping muffins.

Chill the cream cheese filling: It’s tempting to skip chilling, but cooling it gives that luscious, defined cheesecake layer that stays creamy without melting completely.
Don’t overmix the batter: Overworking the flour makes muffins tough—fold gently until just combined.
Pat the streusel gently: Press it lightly into the batter so it sticks and creates that perfect crumbly top.
Check baking early: Especially if your cream cheese is softer than usual, start checking a few minutes before the recommended time to avoid overbaking.

How to Serve Pumpkin Cheesecake Muffins with Streusel Recipe

Pumpkin Cheesecake Muffins - Serving Suggestion

Garnishes

When serving, I love to dust the tops lightly with a bit of ground cinnamon and raw turbinado cane sugar before anyone sees them. It adds just the right sparkle and a hint of extra crunch that makes every muffin look gourmet—even when you’re serving it with a cup of coffee at home.

Side Dishes

These muffins pair beautifully with a creamy chai latte or a simple vanilla bean coffee. If you’re hosting brunch, a fresh fruit salad with autumn fruits like pears, apples, and pomegranate arils complements the warm spices perfectly.

Creative Ways to Present

For a holiday gathering, I like to set these muffins out on a wooden board with small bowls of extra streusel, whipped cream, and a drizzle of maple syrup. It turns a simple muffin into a festive station where guests can customize their bites. You can also stack mini versions on a tiered cake stand for a charming centerpiece treat.

Make Ahead and Storage

Storing Leftovers

I usually keep leftover muffins in an airtight container in the fridge. They’re best eaten within 3 to 5 days. When stacking them, I place parchment or wax paper between layers to keep the streusel topping intact. Just let them warm up at room temperature for 15 minutes before serving, or microwave for 10–15 seconds to enjoy that freshly baked feel.

Freezing

If I’m making a big batch (which happens often!), I freeze the muffins in a single layer inside a sealed freezer bag. They keep well for up to 3 months. When ready to enjoy, I thaw them overnight in the fridge and then warm them briefly in the microwave.

Reheating

Microwaving for 10 to 20 seconds does the trick perfectly without drying the muffins out. I like to cover them loosely with a damp paper towel to keep moisture in, so each bite tastes almost like fresh from the oven.

Frequently Asked Questions:

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

It’s best not to use canned pumpkin pie mix because it already contains sweeteners and spices, which will throw off the balance of flavors in this recipe. Stick to pure pumpkin puree for the best results.

How do I prevent the cream cheese filling from leaking out?

Make sure your cream cheese filling is chilled enough to hold its shape during baking. Also, layering the cream cheese filling between the pumpkin batter, as the recipe explains, helps contain it so it doesn’t ooze out.

Can I make these muffins gluten-free?

You can substitute a 1-to-1 gluten-free flour blend for all-purpose flour, but expect a slightly different texture. Make sure your blend contains xanthan gum to help with structure and moisture retention.

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

For the most accurate results, weigh your flour on a kitchen scale; the recipe calls for 324 grams. Alternatively, fluff the flour, spoon it lightly into your measuring cup, and level it off with a knife instead of scooping directly from the bag. This prevents compacting, which can lead to dense muffins.

Final Thoughts

Honestly, these Pumpkin Cheesecake Muffins with Streusel Recipe have become my go-to for both everyday treats and special occasions. They capture the cozy, sweet, and slightly spicy essence of fall in a way that always feels elevated yet approachable. Whether you whip them up for a weekend brunch or a last-minute gift, they’ll bring smiles and requests for seconds. I can’t wait for you to try this recipe and make it your own!