If you’re searching for that perfect autumn treat or simply craving something soft, sweet, and filled with cozy flavors, these Gluten-Free Pumpkin Cream Cheese Muffins are a dream come true. With a tender crumb, a swirl of tangy cream cheese, and a gorgeous pumpkin spice aroma, they check every box for comfort and indulgence—without a trace of gluten. Whether you’re baking for breakfast, brunch, or an afternoon snack, these muffins bring together simple ingredients for stunning results you’ll want to savor year-round.

Gluten-Free Pumpkin Cream Cheese Muffins Recipe - Recipe Image

Ingredients You’ll Need

The irresistible flavor and texture of these muffins come from a thoughtful blend of pantry staples. Each ingredient plays a starring role in making the Gluten-Free Pumpkin Cream Cheese Muffins moist, flavorful, and utterly delightful. Take a peek at what you’ll need and a few tips to make the most of them!

Gluten-free all-purpose flour (with xanthan gum): This provides the perfect base, giving structure without any gluten—make sure it contains xanthan gum so your muffins stay fluffy, not crumbly!
Baking soda & baking powder: This duo lifts the muffins, keeping them tall and light rather than dense.
Salt: Just a pinch heightens every flavor and balances the sweetness beautifully.
Pumpkin pie spice: The magic ingredient for rich autumnal warmth in every bite.
Ground cinnamon: Enhances the overall spice profile and fills your kitchen with that inviting aroma.
Canned pumpkin puree: The all-star for texture and moisture, plus that unmistakable pumpkin flavor (don’t use pie filling here!).
Brown sugar: Adds sweetness and a touch of caramel depth that’s irresistible in muffins.
Vegetable oil: Keeps every bite gloriously tender and helps with the lovely crumb.
Large eggs: Bind everything together and provide a little rise for those signature muffin domes.
Vanilla extract: Layers in warming aroma and rounds out the flavor.
Cream cheese (softened): The creamy, tangy swirl surprises in the center and pairs perfectly with pumpkin.
Granulated sugar: Sweetens the filling just enough for that classic cheesecake taste.
Extra vanilla extract (for filling): Lends an extra layer of aromatic sweetness to the creamy center.

How to Make Gluten-Free Pumpkin Cream Cheese Muffins

Step 1: Prep Your Oven and Muffin Tin

Kick things off by preheating your oven to 350°F (175°C). This ensures even baking and steady rise. Line a 12-cup muffin tin with paper liners to prevent sticking and create that iconic muffin look—plus cleanup is a breeze!

Step 2: Whisk Together the Dry Ingredients

In a medium bowl, whisk together the gluten-free all-purpose flour (with xanthan gum), baking soda, baking powder, salt, pumpkin pie spice, and ground cinnamon. This step ensures your leaveners and spices are perfectly distributed, creating muffins that bake up evenly spiced and beautifully textured.

Step 3: Combine the Wet Ingredients

In a large mixing bowl, blend the pumpkin puree, brown sugar, vegetable oil, eggs, and vanilla extract. Stir until the mixture is completely smooth—this is your flavor-packed base that guarantees each muffin is moist and delicious.

Step 4: Mix Together the Muffin Batter

Gradually fold the dry ingredients into the wet mixture. Gentle mixing is key here—stop as soon as you don’t see any streaks of flour. This keeps your Gluten-Free Pumpkin Cream Cheese Muffins soft and tender, never tough or dense.

Step 5: Prepare the Cream Cheese Filling

In a separate small bowl, use a hand mixer or sturdy spoon to beat the softened cream cheese with granulated sugar and vanilla extract. You’ll want this filling to be smooth and spreadable for that dreamy cheesecake swirl.

Step 6: Assemble the Muffins

Spoon about a tablespoon of muffin batter into each paper liner. Add a heaping teaspoon of cream cheese filling right in the center (try not to let it touch the sides for best results), then cover with another tablespoon of batter—make sure the filling is mostly enclosed. If you’re feeling fancy, swirl the tops gently with a toothpick for a marbled effect.

Step 7: Bake and Cool

Bake your muffins for 18 to 22 minutes, or until a toothpick inserted near the edge comes out clean (avoid the direct center since the cream cheese will be gooey). Let them cool in the pan for 5 minutes, then remove to a wire rack to cool completely. This helps keep those irresistible muffin tops perfectly shaped and prevents soggy bottoms.

Step 8: Enjoy!

Once cooled, dive in—these Gluten-Free Pumpkin Cream Cheese Muffins are best enjoyed fresh, but they’re just as good for a quick breakfast or cozy snack the next day.

How to Serve Gluten-Free Pumpkin Cream Cheese Muffins

Garnishes

A little extra flair never hurts! Sprinkle your muffins with a dusting of cinnamon sugar before baking for a crisp, sweet topping. If serving later, a light drizzle of maple glaze or a few toasted pepitas on top can really make them pop, both visually and flavor-wise.

Side Dishes

Pair your Gluten-Free Pumpkin Cream Cheese Muffins with a creamy chai latte, hot coffee, or spiced apple cider for an incredible brunch spread. If you love a savory touch, serve alongside scrambled eggs or a fresh, herby salad to balance out the sweetness.

Creative Ways to Present

Stack muffins high on a rustic cake stand for a festive breakfast display, or line individual muffins on a pretty platter for grab-and-go convenience at a fall party. You can even wrap cooled muffins in parchment and twine for a charming homemade gift that anyone would appreciate!

Make Ahead and Storage

Storing Leftovers

Keep your leftover Gluten-Free Pumpkin Cream Cheese Muffins fresh by placing them in an airtight container in the refrigerator. They’ll stay delicious for up to 4 days. The cream cheese filling means refrigeration is a must to maintain both taste and food safety.

Freezing

To freeze, wait until the muffins are completely cool, then wrap them individually in plastic wrap and store in a freezer-safe bag or container. They’ll hold up well for up to 2 months—perfect for popping one out whenever a pumpkin craving strikes!

Reheating

Reheat refrigerated muffins by microwaving for 15 to 20 seconds for that just-baked warmth and softness. If reheating from frozen, let thaw overnight in the refrigerator first, then warm in the microwave or a low oven until gently heated through.

FAQs

Can I make these muffins dairy-free?

Absolutely! Substitute the cream cheese with a dairy-free cream cheese alternative and use a plant-based oil (like canola or avocado) to keep everything moist and tender. You’ll still get a delightful swirl and that signature muffin texture.

Do I need to use canned pumpkin or can I use homemade pumpkin puree?

Either one works! Just make sure homemade pumpkin puree is well-drained and not watery, or your muffins could end up too moist. Canned pumpkin offers consistency in color and flavor if you want guaranteed results every time.

Why do I need xanthan gum in my gluten-free flour?

Xanthan gum is the secret weapon for gluten-free baking. It mimics the elasticity of gluten, holding your Gluten-Free Pumpkin Cream Cheese Muffins together so they don’t fall apart—this means a tender crumb, not a crumbly mess.

Can I add nuts or chocolate chips to this recipe?

Of course! Fold in a handful of toasted pecans, walnuts, or mini chocolate chips for a tasty twist. Just be mindful not to overload the batter so your muffins bake up fluffy and light.

How can I make mini muffins instead of full-size?

Simply portion the batter and cream cheese filling into a mini muffin tin and reduce the baking time to about 10–12 minutes. They’ll be adorable party-ready bites with all the flavor of full-sized Gluten-Free Pumpkin Cream Cheese Muffins.

Final Thoughts

Every bite of these Gluten-Free Pumpkin Cream Cheese Muffins bursts with cozy fall flavor and creamy-goodness, making them a must-bake for anyone craving something sweet, satisfying, and gluten-free. Give them a try and watch how quickly they disappear from your kitchen counter—they’re destined to become a new favorite, no matter the season!

Gluten-Free Pumpkin Cream Cheese Muffins Recipe

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4.5 from 5 reviews

Author: admin
Total Time: 35 minutes
Yield: 12 muffins 1x
Diet: Gluten-Free, Vegetarian

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Description

Delicious gluten-free pumpkin muffins with a decadent cream cheese filling, perfect for fall baking or anytime you want a tasty treat. These moist and flavorful muffins are a delightful combination of pumpkin spice and creamy indulgence.

Ingredients

Scale

For the Muffins:

1 1/2 cups gluten-free all-purpose flour (with xanthan gum)
1/2 teaspoon baking soda
1/2 teaspoon baking powder
1/4 teaspoon salt
1 teaspoon pumpkin pie spice
1/2 teaspoon ground cinnamon
2/3 cup canned pumpkin puree
2/3 cup brown sugar
1/4 cup vegetable oil
2 large eggs
1 teaspoon vanilla extract

For the Cream Cheese Filling:

4 oz cream cheese, softened
2 tablespoons granulated sugar
1/2 teaspoon vanilla extract

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Instructions

Preheat the oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners.
In a medium bowl, whisk together the gluten-free flour, baking soda, baking powder, salt, pumpkin pie spice, and cinnamon.
In a large bowl, combine the pumpkin puree, brown sugar, oil, eggs, and vanilla extract. Stir until smooth.
Gradually add the dry ingredients to the wet, mixing until just combined.
In a separate small bowl, beat the cream cheese, sugar, and vanilla extract until smooth.
Spoon a tablespoon of muffin batter into each liner, then add about a teaspoon of cream cheese filling to the center. Cover with another tablespoon of batter, making sure the filling is mostly enclosed.
Bake for 18–22 minutes, or until a toothpick inserted near the edge (not the center) comes out clean.
Let cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.