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

Imagine biting into a tender muffin that’s bursting with cozy spices, smooth cream cheese, and a delightful crunchy streusel on top—*that’s* the magic of this Pumpkin Cheesecake Muffins with Streusel Topping Recipe. It’s one of those treats that tastes as complex as it sounds but is delightfully simple to make once you have the right steps.

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

Every time I make this Pumpkin Cheesecake Muffins with Streusel Topping Recipe, it feels like a little celebration in my kitchen. The combination of pumpkin spice, creamy cheesecake, and that crunchy pecan streusel topping is pure comfort. Plus, they’re perfect for breakfast, snack, or dessert.

Irresistible Flavor Combo: The pumpkin and cream cheese filling create a moist, tangy center that pairs wonderfully with the sweet, crumbly streusel.
Great Texture Contrast: Soft, tender muffin base with a creamy filling and crunchy topping that keeps every bite interesting.
Make-Ahead Friendly: You can prepare components in advance to save time and bake fresh muffins anytime you want.
Perfect for Gifting: These muffins are fancy enough to impress friends but easy enough to whip up on a busy morning.

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

This recipe really shines because the ingredients each have a purpose — from the cream cheese that gives lusciousness, to the spices that create that iconic pumpkin flavor, and finally the streusel topping that adds texture. Here’s a quick rundown of the essentials and why I stick to them.

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: Full-fat block cream cheese gives the filling that rich, tangy flavor and creamy texture without being too soft or runny.
Pecans: Raw pecan halves add crunch and a nutty warmth to the streusel, but you can swap in walnuts if you prefer.
Pumpkin Puree: Use pure pumpkin puree (Libby’s is my go-to) for authentic flavor; avoid pumpkin pie filling since it has added sugar and spices.
Spices: Cinnamon, nutmeg, cloves, and ginger bring all the cozy fall warmth we expect from pumpkin treats.
Butter: Cold, cubed butter is key for that pebble-like streusel texture — don’t melt it or your topping won’t have the right crunch.
Flour: Accurate measuring is important for light muffins; I recommend weighing if you can, but if not, fluff and spoon into the cup gently.
Sugars: Brown and granulated sugars balance sweetness and depth — the brown sugar also helps the streusel caramelize nicely.
Eggs & Oil: Create a tender, moist muffin base without weighing it 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 love how versatile this Pumpkin Cheesecake Muffins with Streusel Topping Recipe is — I often tweak it based on what I have in the pantry or the occasion. You should feel free to customize it too, whether you want more spice, a nut-free option, or a lighter version.

Nut-Free Version: I once made these for a friend with a nut allergy, swapping the pecans for toasted oats in the streusel — still delicious but safer for them.
Extra Spice Kick: If you like your pumpkin spice bolder, I add a bit more cinnamon and a dash of cardamom — it perks up the flavor wonderfully.
Mini Muffins: Perfect for parties! Just reduce baking time to about 15 minutes and watch closely for that toothpick test.
Swirl It Up: Try swirling the cream cheese filling into the pumpkin base instead of layering — I do this when I want a marbled look that’s equally tasty.

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

Step 1: Whip Up The Cream Cheese Filling

Start by softening your cream cheese at room temperature — this really matters. Then whisk it together with powdered sugar and vanilla until smooth; it’ll be thick but scoopable. I like to pop my filling in the freezer for 20-30 minutes so it firms up a bit; this helps it hold shape inside the muffins while baking.

Step 2: Prepare the Streusel Topping

Throw your pecans in a food processor and pulse them a few times — you want small chunks, not dust. Next, add the dry ingredients (flour, sugars, cinnamon) and pulse again to combine. Finally, sprinkle your cold cubed butter on top and pulse until the mixture looks like coarse crumbs or “small pebbles.” If you see larger butter chunks, pinch them between your fingers in the mixture. Freeze this topping while you tackle your muffin batter.

Step 3: Mix the Muffin Batter

In one bowl, whisk your eggs gently then mix in sugar, pumpkin puree, and oil until smooth. In another, combine your flour with baking soda, baking powder, salt, and all your warming pumpkin spices. Slowly add the dry to the wet, stirring just enough to combine — overmixing is the enemy here because it can make the muffins tough.

Step 4: Assemble the Muffins

Line your muffin tin with paper liners and lightly spray them to prevent sticking. Spoon about 1½ tablespoons of batter into the bottom of each cup and spread to cover the base. Then add a rounded tablespoon of cream cheese filling right in the center. Top the cream cheese with the remaining batter, covering it completely. Finally, sprinkle a generous tablespoon of the streusel topping evenly over each muffin and press it gently into the batter so it bakes in place instead of falling off.

Step 5: Bake and Cool

Bake at 350°F (175°C) for 20–22 minutes. The baking time varies depending on how chilled your cream cheese filling is — softer filling means longer bake time. Check doneness by inserting a toothpick into the muffin top (avoiding cream cheese); it should come out clean or with a few moist crumbs. Let the muffins cool in the pan for about 5 minutes before moving them to a wire rack. If you want, sprinkle with a little cinnamon and raw cane sugar while still warm for that extra sparkle.

Top Tip

From my time perfecting this recipe, these nuggets of wisdom will save you frustration and help your muffins turn out bakery-quality every time.

Perfect Cream Cheese Consistency: Avoid cream cheese that’s too cold or too warm — room temperature (but still firm) is your sweet spot to get a filling that melts just right inside the muffin.
Measuring Flour Correctly: I’ve learned not to scoop the flour with the measuring cup directly — always fluff and spoon it gently to avoid dense muffins.
Keep Butter Cold for Streusel: If your butter softens too much, your topping loses that satisfying crumbly texture, so cube and chill it right before pulsing.
Watch Your Baking Time: Because cream cheese takes heat differently than batter, don’t rely only on baking time—always check with a toothpick for the best result.

How to Serve Pumpkin Cheesecake Muffins with Streusel Topping Recipe

pumpkin cheesecake muffins - Serving Suggestion

Garnishes

Sometimes I like a dusting of cinnamon or a sprinkling of turbinado sugar right after baking for a bit of sparkle and extra crunch. A drizzle of honey or maple syrup can also add a lovely sweet finish if you want more indulgence.

Side Dishes

These muffins pair wonderfully with a simple cup of black coffee or chai latte. If it's breakfast, a side of Greek yogurt topped with fresh berries balances the rich cream cheese perfectly.

Creative Ways to Present

For gatherings, I’ve arranged these muffins on a rustic wooden board topped with sprigs of fresh rosemary and miniature pumpkins for a festive fall look. They’re also beautiful served warm in decorative cupcake wrappers and tied with twine for gifting.

Make Ahead and Storage

Storing Leftovers

I usually let these muffins cool completely, then store them in an airtight container in the fridge for up to 5 days. I like to layer them with parchment paper to prevent sticking — this keeps the streusel crisp and the filling fresh.

Freezing

They freeze beautifully! I wrap each muffin individually in plastic wrap, then place them in a freezer-safe bag. When you want one, just thaw at room temperature or microwave gently — no soggy crumbs here.

Reheating

To get that fresh-out-of-the-oven warmth, I microwave a muffin for about 10 seconds on high. If you want a crispier streusel, a quick 3-5 minute toast in a preheated 325°F oven does the trick.

Frequently Asked Questions:

Can I use canned pumpkin pie filling instead of puree?

You shouldn't because canned pumpkin pie filling contains added sugar, spices, and sometimes preservatives that can change the texture and sweetness of the muffins. Stick to pure pumpkin puree for the best flavor and consistency.

How do I know when the muffins are done baking?

Since these muffins contain a cream cheese filling, the best way to check doneness is to insert a toothpick into the cake portion of the muffin, avoiding the filling center. The toothpick should come out clean or with just a few moist crumbs. If you poke into the cream cheese, the toothpick will be wet even when the muffin is done.

Can I make these muffins gluten-free?

Yes! Substitute the all-purpose flour with a quality gluten-free baking blend that is meant for a 1:1 substitution. Make sure your blend contains xanthan gum or another stabilizer to help maintain texture and structure. Baking time might vary slightly.

How do I store these muffins to keep them fresh longer?

After baking and cooling, store the muffins in an airtight container in the refrigerator. If stacking, separate layers with parchment or wax paper to keep the streusel topping intact. They last 3-5 days refrigerated and can be warmed slightly before serving.

Final Thoughts

These Pumpkin Cheesecake Muffins with Streusel Topping have become my go-to for fall mornings and anytime I want a comforting treat with a little extra wow factor. They’re approachable, forgiving, and simply delicious. Give them a try—you’ll be amazed by how easy it is to nail a bakery-worthy muffin right in your own kitchen, and trust me, your friends won’t stop asking for the recipe.