Name: Pumpkin Cheesecake Muffins with Pecan 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 so indulgent about the combination of pumpkin and cream cheese, especially with a crunchy pecan streusel on top. This Pumpkin Cheesecake Muffins with Pecan Streusel Recipe is where spiced autumn flavors meet creamy, dreamy texture—a treat you’ll be excited to make again and again.

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

Why You'll Love This Recipe

These muffins quickly became one of my favorite ways to enjoy pumpkin season with something a little more special than your typical pumpkin bread. I love how the cream cheese swirls inside each muffin, offering pockets of soft, tangy goodness that pair perfectly with the nutty pecan topping.

Layered flavors and texture: Creamy cheesecake filling with moist pumpkin muffin and crunchy pecan streusel is simply irresistible.
Perfect portion control: Muffins are easy to share and great for breakfasts, snacks, or dessert on the go.
Impressive but easy to make: It looks like a bakery treat, but it’s totally doable in your kitchen with everyday ingredients.
Customizable for your preferences: You can tweak the spices, swap nuts, or adjust the sweetness just how you like it.

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

Each ingredient in this Pumpkin Cheesecake Muffins with Pecan Streusel Recipe plays a role in making these muffins perfectly tender, flavorful, and satisfying. Getting to know your ingredients helps you understand why this recipe works so well and how you can make your own creative tweaks.

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

Cream cheese: Full-fat is key for the luscious filling to maintain its softness and slight tang after baking.
Powdered sugar: Dusting the cream cheese ensures smooth, lump-free filling that's not too gritty.
Raw pecans: Give the topping a rich crunch and buttery flavor; pulsing them 3 times keeps an ideal texture.
Flour: All-purpose gives structure to muffins; weighing or proper measuring avoids dry or heavy results.
Libby’s pumpkin puree: This puree is ideal due to its consistency and moisture balance for perfect muffin texture.
Spices (cinnamon, nutmeg, cloves, ginger): Warming spices evoke that classic pumpkin pie flavor everyone loves.
Cold butter: Cut into the topping for a tender crumb that crisps up nicely in the oven.
Eggs and oil: Help bind and keep the muffins moist without making them dense.
Sugars (granulated and brown): Balance sweetness and deepen the flavor complexity, especially in the streusel.

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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

While I stick close to the original recipe when baking for family, I love experimenting with little tweaks that tailor these muffins to different moods or dietary needs. Feel free to make it truly yours!

Variation: I sometimes swap pecans for walnuts or add a few chocolate chips under the streusel for a touch of surprise sweetness.
Dairy-Free Option: Using vegan cream cheese and a plant-based butter alternative in the streusel works well with minor flavor differences.
Spice Adjustments: If you want a milder profile, reduce cloves and nutmeg by half; for a bolder kick, add a pinch of freshly grated ginger.
Make It Mini: Try these as mini muffins for parties—a perfect bite-size treat that’s gone in seconds!

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

Step 1: Whip Up the Cream Cheese Filling

Start by softening your cream cheese at room temperature—that’s important for a smooth filling. Mix the cream cheese with powdered sugar and vanilla, whisking well until silky. It will take some elbow grease if you don't have a mixer handy. Pop this into the freezer while you work on the rest so it firms up just enough to scoop easily without melting into the batter prematurely.

Step 2: Make the Pecan Streusel Topping

Pulse pecans a few times in your food processor to get a rough chop—not too fine! Add flour, sugars, and cinnamon, then pulse to blend. Sprinkle the cold, cubed butter on top and pulse until it looks like small pebbles with some little butter pieces. Those buttery bits are magic—they melt into a perfect crumb while baking. If you're in a pinch or don’t have a processor, cutting in the butter by hand with a pastry cutter works just as well.

Step 3: Prepare the Pumpkin Batter

Preheat your oven to 350°F and line two muffin tins with liners, giving them a quick spray to stick-proof. Whisk the eggs gently, then mix them with sugar, pumpkin puree, and oil until smooth. In another bowl, whisk together the dry ingredients carefully measured—the spices are key here for flavor depth. Combine the dry mix with the wet, folding just enough to blend the batter without overmixing.

Step 4: Assemble the Muffins for Baking

Scoop about 1½ tablespoons of pumpkin batter into each muffin liner and spread it thin to cover the bottom. Next, gently add a rounded tablespoon of cream cheese filling on top—don’t worry if it looks thick, it melts beautifully during baking. Cover with the remaining pumpkin batter, then top generously with about a heaping tablespoon of pecan streusel. Press the streusel lightly into the batter, so it sticks well and doesn't fall off.

Step 5: Bake and Cool

Bake for 20-22 minutes at 350°F. The baking time can vary based on how chilled your cream cheese filling is—softer filling means a slightly longer bake. The best test is to insert a toothpick into the muffin’s top layer, avoiding the cream cheese center; it should come out clean. Let your muffins cool for 5 minutes in the pan before transferring them to a wire rack. Sprinkle with cinnamon and raw turbinado sugar if you like a dreamy sparkle and extra crunch.

Top Tip

After trying this recipe many times, I've found a few simple tricks that really up the game and help avoid common muffin mishaps.

Correct Cream Cheese Temperature: Room temp is your friend here; too cold and it won’t blend properly, too warm and it’ll melt into the batter instead of forming that lovely swirled filling.
Measure Flour Accurately: Fluff, spoon, and level! Scooping flour directly from the bag packs it too much, leading to dry, dense muffins.
Chill Streusel Butter: Keep butter cold until pulsing or cutting in—this ensures a crumbly topping that crisps up beautifully rather than melting flat.
Don’t Overmix Batter: Stir just until combined to keep muffins tender and avoid tough, rubbery texture.

How to Serve Pumpkin Cheesecake Muffins with Pecan Streusel Recipe

Pumpkin Cheesecake Muffins - Serving Suggestion

Garnishes

I love sprinkling a little coarse turbinado sugar and cinnamon right after baking—it adds a subtle crunch and that cozy spice aroma that gives these muffins an extra touch of warmth. Sometimes, a light drizzle of maple syrup or a dollop of whipped cream on the side turns these into an elegant brunch treat.

Side Dishes

Pairing these muffins with a cup of spiced chai or freshly brewed coffee makes for a lovely morning or afternoon break. For a heartier spread, sliced apples with cinnamon or a bowl of homemade granola complements the pumpkin’s sweetness beautifully.

Creative Ways to Present

For holiday gatherings, I've arranged Pumpkin Cheesecake Muffins with Pecan Streusel Recipe on a tiered stand surrounded by autumn leaves and cinnamon sticks — it’s such a feast for the eyes. You can also pop them in mini cupcake liners decorated with fall motifs for kids' parties or bake them in a silicone muffin tray for a fun shape twist.

Make Ahead and Storage

Storing Leftovers

Once cooled, I store leftover muffins in an airtight container in the fridge to keep the cream cheese filling fresh and safe. If I’m stacking them, I put parchment paper between layers—this prevents the crumb topping from sticking together and losing its crisp texture.

Freezing

These muffins freeze beautifully! After cooling completely, wrap each one individually in plastic wrap, then place them in a freezer-safe bag. When you want one, thaw at room temperature or pop it in the microwave for about 15 seconds—no one will guess they were frozen.

Reheating

I usually microwave for 10-15 seconds just to take the chill off, which helps restore that soft, fresh-from-the-oven texture. Avoid over-heating or your crumb topping can lose its crunch, so a gentle warm-up is best.

Frequently Asked Questions:

What if I don’t have a food processor for the pecan streusel?

You can easily make the streusel by combining the chopped pecans, sugars, spices, and flour in a bowl, then cutting in the cold butter with a pastry cutter or two forks until the mixture forms small crumbs. This method works just as well as pulsing in a food processor and still creates a perfect crumb topping.

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

It’s best to use pure pumpkin puree rather than pumpkin pie filling, as pie filling contains added sugars and spices that would throw off the recipe’s balance. If you only have pie filling, reduce the sugar in the batter accordingly and omit or reduce the spices to avoid overly sweet or spiced muffins.

How do I make sure the cream cheese filling stays inside the muffin and doesn’t leak?

Chilling the cream cheese filling until it’s firm but scoopable is key. If it’s too soft, it can melt and spread during baking. I recommend freezing the cream cheese filling for about 20–30 minutes after mixing to achieve the perfect consistency that holds up through baking.

Can I make these muffins vegan or gluten-free?

Totally! For a vegan version, substitute plant-based cream cheese and butter substitutes, and use flax eggs or another egg replacer. Gluten-free all-purpose flour blends can replace regular flour, but I suggest checking the blend is suited for baking with yeast or rise. You might get a slightly different texture, but the muffins will still be delicious!

Final Thoughts

This Pumpkin Cheesecake Muffins with Pecan Streusel Recipe is like a cozy hug in muffin form, blending creamy, nutty, and warmly spiced flavors that always put a smile on my face and those I serve. I can’t recommend trying this recipe enough — it’s an approachable yet impressive way to celebrate pumpkin season or any time you want a little something special. Roll up your sleeves and give it a go; I’m pretty sure you’ll fall in love just like I did.