Name: Pumpkin Cream Cheese Muffins 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 comforting about the warm, cozy flavors of fall baked into a muffin, especially when that velvety cream cheese surprise awaits inside. This Pumpkin Cream Cheese Muffins Recipe truly elevates classic pumpkin muffins with a luscious, creamy center and a crunchy pecan streusel topping that’ll have you baking 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 Cream Cheese Muffins Recipe
Top Tip
How to Serve Pumpkin Cream Cheese Muffins Recipe
Make Ahead and Storage
Frequently Asked Questions:
Final Thoughts
Pumpkin Cream Cheese Muffins Recipe

Why You'll Love This Recipe

I honestly can't say enough good things about this Pumpkin Cream Cheese Muffins Recipe. What really drew me in the first time I made them was how the flavors and textures perfectly balance each other — a tender pumpkin muffin surrounded by a tangy, creamy cheesecake center, finished with a buttery pecan crumble. Plus, they’re easier to make than they look!

Cream Cheese Surprise: The luscious, slightly tangy cream cheese filling adds a beautifully unexpected twist inside each muffin.
Crunchy Topping: The pecan streusel topping gives a perfect crunch contrast to the soft, moist pumpkin muffin.
Rich Flavor Profile: A blend of fall spices complements the pure pumpkin, making every bite warm and aromatic.
Make-Ahead Friendly: These muffins store well and taste just as good the next day, making them perfect for busy mornings or brunch gatherings.

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 Cream Cheese Muffins Recipe is there for a reason — whether it’s flavor, texture, or to make sure everything holds together beautifully. I’ve found that using full-fat cream cheese and pure pumpkin puree really makes a difference in taste and consistency.

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: Use full-fat and let it soften properly for a creamy, smooth filling that won’t leak out during baking.
Powdered Sugar: Adds sweetness without graininess, perfect for that silky cheesecake layer.
Vanilla Extract: Enhances the overall flavor, adding warmth and depth.
Raw Pecan Halves: For that irresistible crunch in the streusel topping — toast them lightly for extra nuttiness.
Flour: All-purpose flour provides structure, but be sure to measure correctly to avoid dense muffins.
Brown Sugar & Granulated Sugar: Together they give a complex sweetness and help with the moist crumb and topping.
Cinnamon, Cloves, Nutmeg, Ginger: Classic fall spices that make these muffins unmistakably seasonal and cozy.
Eggs: Bind everything together and add richness.
Vegetable Oil: Keeps muffins moist and tender without overpowering flavor.
Libby’s Pure Pumpkin Puree: I stick with this brand for its consistent texture and flavor; if you use another, blot the puree to avoid excess moisture.
Cold Butter: Crucial for that crumbly, buttery streusel topping.

📝

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 love the classic version as made here, one of the joys of this Pumpkin Cream Cheese Muffins Recipe is how easy it is to customize. Feel free to adjust the spices or toppings, or try swapping out nuts based on what you have handy!

Variation: I've swapped pecans for walnuts plenty of times — toasty walnuts add a slightly earthier flavor that’s just as delicious.
Dairy-Free: For a dairy-free version, you could use vegan cream cheese and coconut oil in place of butter, though the texture shifts slightly.
Spice Level: Mix in a little extra ginger or add allspice for a unique twist that amps up the fall warmth.
Sweetener Swap: I sometimes cut back the sugar or use maple sugar for a natural sweet twist that pairs beautifully with pumpkin.

Step-by-Step: How I Make Pumpkin Cream Cheese Muffins Recipe

Step 1: Whip Up the Cream Cheese Filling

Start by softening your cream cheese until it's just pliable but not melting — this is key for that luscious filling. Mix it with powdered sugar and vanilla until super smooth. I usually whisk by hand because it helps me feel the texture, but a handheld mixer works too. Pop this in the freezer for about 20 minutes to firm up slightly before using.

Step 2: Prepare the Streusel Topping

Toast the pecans slightly in a dry pan or the oven before pulsing them in your food processor. Add the flour, sugars, and cinnamon, then quickly pulse in cold, cubed butter until the mixture forms little clumps that resemble coarse gravel. If you're going old school, cutting butter into the dry ingredients with a pastry cutter works great too! Toss this in the freezer while you move on.

Step 3: Combine Wet Ingredients

In a large bowl, lightly whisk your eggs, then add sugar, pumpkin puree (blotted if using a different brand for less moisture), and vegetable oil. Mix until smooth and combined — this is the flavorful base that gives your muffins moisture and tenderness.

Step 4: Mix Dry Ingredients Separately

In another bowl, sift together all-purpose flour, baking soda, baking powder, salt, and the warm spices. Taking this step separately helps evenly distribute the leaveners and spices, ensuring perfect texture and flavor.

Step 5: Bring It Together & Assemble

Gently fold the dry ingredients into the wet pumpkin mixture — mix just until combined to keep your muffins tender. Then, scoop about 1½ tablespoons of batter into each muffin cup, smoothing the bottom. Drop a tablespoon of the cream cheese filling over that, then cover with more pumpkin batter. Top with a generous spoonful of the pecan streusel and gently press it down so it bakes into the muffin instead of falling off.

Step 6: Bake and Cool

Bake at 350°F for 20-22 minutes, but keep an eye on them depending on how chilled your cream cheese filling is. The filling tends to affect the bake time, so test with a toothpick carefully, avoiding the cream cheese part. Once baked, cool for 5 minutes in the tin, then transfer to a rack to cool completely. A quick sprinkle of cinnamon and raw cane sugar adds the perfect finishing touch.

Top Tip

From the many batches I've baked, these tips will help you nail this Pumpkin Cream Cheese Muffins Recipe every single time.

Cream Cheese Consistency: Make sure the cream cheese filling is stiff but scoopable before baking. If it’s too soft, the filling could melt into the batter or melt out during baking, leading to a less defined center.
Measure Flour Carefully: I’ve learned the hard way that too much flour makes muffins dense. Fluff the flour, spoon it into your measuring cup, then level it off instead of scooping directly.
Don’t Overmix Batter: Mix dry into wet just until combined. Overmixing activates gluten, making muffins tougher. It’s okay to see some streaks, they’ll bake out.
Check Doneness Carefully: Avoid poking the filling with your toothpick test — that won’t give an accurate read. Instead, test the cake part near the edge of the muffin.

How to Serve Pumpkin Cream Cheese Muffins Recipe

pumpkin cream cheese muffins - Serving Suggestion

Garnishes

I love sprinkling these muffins with a little ground cinnamon and coarse raw turbinado sugar right after baking for that sparkly, slightly crunchy top. Sometimes, a little dollop of maple butter or honey butter on the side makes them feel extra special.

Side Dishes

Pair these muffins with a warm cup of chai tea or coffee for a perfect autumn breakfast or snack. They also go nicely alongside a creamy soup, like butternut squash or pumpkin soup, if you're serving them as part of an afternoon spread.

Creative Ways to Present

For holidays or gatherings, I arrange these muffins on a rustic wooden board surrounded by small bowls of spiced cream cheese, chopped nuts, and a drizzle station with maple syrup and honey. It makes for a delightful, interactive way to enjoy them with guests!

Make Ahead and Storage

Storing Leftovers

I keep leftover Pumpkin Cream Cheese Muffins tightly sealed in an airtight container, lined with parchment paper if I’m stacking. They stay fresh in the fridge for about 3 to 5 days. Let them come back to room temp or warm for that “freshly baked” feel when enjoying later.

Freezing

These muffins freeze wonderfully—wrap each muffin in plastic wrap and put them in a zip-top bag or container. When you want one, thaw at room temperature or warm slightly in the microwave. The cream cheese filling holds up beautifully, making this a perfect make-ahead treat.

Reheating

To reheat, I usually pop a muffin in the microwave for about 10-15 seconds—just enough to soften the cream cheese center and bring out the pumpkin aroma. Avoid overheating or they can dry out, so watch closely!

Frequently Asked Questions:

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

Canned pumpkin pie filling is sweetened and spiced, so it’s not ideal for this Pumpkin Cream Cheese Muffins Recipe. It can throw off the moisture and sweetness levels. Stick with pure pumpkin puree for best flavor and texture.

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

Make sure the cream cheese filling is firm but scoopable before adding it to the batter. Chilling it for 20-30 minutes helps set the shape. Also, be gentle when layering the batter so the filling doesn’t mix with the pumpkin too much, which can cause leaking.

Can I make this recipe gluten-free?

Absolutely! Substitute the all-purpose flour with a 1:1 gluten-free baking flour blend that contains xanthan gum. This will keep the muffins tender and hold them together well. Baking times might be a touch longer, so keep an eye on them.

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

Fluff the flour in its container, then spoon it gently into your measuring cup and level off the top with a knife. Avoid scooping directly with the measuring cup, as compacting flour can lead to using too much and dense muffins.

Final Thoughts

This Pumpkin Cream Cheese Muffins Recipe holds a special place in my kitchen because it captures all the flavors and textures I crave during cooler months — soft pumpkin spice cake with that creamy, rich center and a crunchy, nutty topping. It feels like a little celebration with every bite. I hope you enjoy making and sharing these muffins as much as I do — once you try them, they’ll be your go-to pumpkin treat too!