If you’re on the hunt for a comforting fall treat that’s both indulgent and free from gluten, you’ve hit the jackpot with this Gluten-Free Pumpkin Cream Cheese Muffins Recipe. These muffins charmingly combine the warm, spiced flavors of pumpkin with the rich, tangy swirl of cream cheese, all wrapped in a tender crumb that’s delightfully moist. Whether you’re baking for a cozy brunch or a midday snack, this recipe brings together simple ingredients to create a truly irresistible experience that everyone will love, gluten intolerance or not.

Ingredients You’ll Need
Gathering these ingredients is a breeze, and each one plays a crucial role in making these muffins spectacular. From the pumpkin puree that delivers moisture and flavor to the cream cheese adding a luscious swirl, every ingredient contributes to the texture, taste, and aroma that make this recipe a standout.
- Gluten-free all-purpose flour (1 1/2 cups): Make sure it contains xanthan gum for the perfect muffin structure.
- Coconut sugar (1/2 cup): Adds natural sweetness with a subtle caramel note, but regular sugar works just fine too.
- Baking soda (1 teaspoon): Helps the muffins rise beautifully and become delightfully fluffy.
- Baking powder (1/2 teaspoon): Gives an extra boost for lightness and lift.
- Ground cinnamon (1 teaspoon): The star spice that brings that cozy, warm flavor we crave in pumpkin treats.
- Ground nutmeg (1/2 teaspoon): Adds depth and a hint of sweetness with its nutty aroma.
- Ground ginger (1/4 teaspoon): Provides a subtle spicy zing that balances the sweetness.
- Salt (1/4 teaspoon): Enhances all the other flavors to perfection.
- Eggs (2 large): Bind the batter and add richness.
- Canned pumpkin puree (1 cup): The moist, flavorful heart of the muffins that’s naturally gluten-free and packed with nutrients.
- Unsweetened applesauce (1/2 cup): Keeps the muffins moist without added fat; you can swap for vegetable oil if preferred.
- Vanilla extract (1 teaspoon): Brings out the sweetness and rounds out the flavors.
- Cream cheese (8 oz, softened): For that decadent cream cheese swirl everyone will adore.
- Powdered sugar (1/4 cup): Sweetens the cream cheese filling just right.
- Vanilla extract (1 teaspoon): Added to the cream cheese mixture for that extra touch of flavor.
How to Make Gluten-Free Pumpkin Cream Cheese Muffins Recipe
Step 1: Preheat and Prepare
Start by preheating your oven to 350°F (175°C). Line your muffin tin with paper liners or grease it with non-stick spray, setting yourself up for an easy release after baking. This step is key for perfectly formed muffins.
Step 2: Mix Dry Ingredients
In a large bowl, whisk together the gluten-free flour, coconut sugar, baking soda, baking powder, cinnamon, nutmeg, ginger, and salt. Getting these dry ingredients evenly combined ensures your muffins bake evenly and develop that signature spiced flavor.
Step 3: Combine Wet Ingredients
In a separate bowl, beat the eggs, pumpkin puree, unsweetened applesauce, and vanilla extract until the mixture is smooth and harmonized. This blend brings moisture, flavor, and tenderness to your muffin batter.
Step 4: Bring It All Together
Gradually add the wet ingredients into the dry ingredients, mixing gently until just combined. The batter will be thick but that’s exactly what you want—over-mixing can make the muffins tough, so keep it light!
Step 5: Prepare the Cream Cheese Swirl
Whip together the softened cream cheese, powdered sugar, and vanilla extract in a small bowl until smooth and creamy. This delicious filling is going to create that dreamy swirl inside each muffin.
Step 6: Assemble Muffins
Spoon about 2 tablespoons of the muffin batter into each muffin cup, then dollop 1 teaspoon of the cream cheese mixture on top. Add more batter to fill the cups about three-quarters full, then use a toothpick to gently swirl the cream cheese into the pumpkin batter for that beautiful marbled effect.
Step 7: Bake Until Perfect
Bake your muffins in the preheated oven for 18-22 minutes. You’ll know they’re done when a toothpick inserted into the center comes out clean, with just that perfect hint of moistness that keeps these muffins so irresistible.
Step 8: Cool Before Enjoying
Let your muffins cool in the tin for about 5 minutes before transferring them to a wire rack to cool completely. This step helps them set so they’re easier to handle and every bite tastes just right.
How to Serve Gluten-Free Pumpkin Cream Cheese Muffins Recipe

Garnishes
These muffins are delightful on their own, but if you want to add a little extra flair, a light dusting of cinnamon sugar or a sprinkle of chopped pecans on top before baking can add a lovely crunch and aromatic sweetness.
Side Dishes
Pair these muffins with a hot cup of chai tea or freshly brewed coffee to enhance their warm spices. They also make a great companion to creamy soups or a fresh, crisp salad for a balanced snack or brunch.
Creative Ways to Present
For a festive touch, serve your gluten-free pumpkin cream cheese muffins on a rustic wooden board with small bowls of honey or maple syrup for drizzling. Wrapping them in parchment paper tied with twine makes for an adorable gift or party favor.
Make Ahead and Storage
Storing Leftovers
Store any leftover muffins in an airtight container at room temperature for up to 3 days. This will keep them moist and flavorful, just like fresh out of the oven.
Freezing
Want to save your muffins for later? They freeze beautifully! Wrap each muffin individually in plastic wrap or foil and place them in a freezer-safe bag for up to 3 months. Thaw overnight in the fridge or at room temperature when ready to enjoy.
Reheating
To warm your muffins back up, pop them in a preheated oven at 325°F (160°C) for about 10 minutes or microwave for 20-30 seconds. This quick heat-up brings back that freshly baked softness you crave.
FAQs
Can I substitute the coconut sugar for something else?
Absolutely! Regular granulated sugar or brown sugar works well and will adjust the flavor slightly but keep the overall sweetness just right.
Is it necessary to use cream cheese in the filling?
The cream cheese swirl is what truly elevates these muffins, providing a rich and tangy contrast. You could experiment with mascarpone or even a dairy-free cream cheese if needed.
What if I don’t have xanthan gum in my gluten-free flour?
Xanthan gum helps bind the ingredients and gives structure. If your flour mix doesn’t include it, add about 1/4 teaspoon per cup of flour to keep the muffins from crumbling.
Can I make these muffins dairy-free?
Yes! Substitute the cream cheese with a dairy-free cream cheese alternative, and use a non-dairy milk if you tweak the wet ingredients accordingly. The flavor will still shine beautifully.
How long do these muffins stay fresh?
When stored properly at room temperature, they stay fresh for about 3 days. For longer storage, freezing is your best bet to maintain moisture and taste.
Final Thoughts
If you’re craving a muffin that feels like a warm hug with every bite, this Gluten-Free Pumpkin Cream Cheese Muffins Recipe is your new best friend. It’s simple, comforting, and loaded with seasonal flavors that brighten any morning or snack time. Don’t hesitate to try this recipe and watch it become a beloved staple in your kitchen!
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Gluten-Free Pumpkin Cream Cheese Muffins Recipe
- Prep Time: 10 minutes
- Cook Time: 20 minutes
- Total Time: 30 minutes
- Yield: 12 muffins 1x
- Category: Baking
- Method: Baking
- Cuisine: American
- Diet: Gluten Free
Description
These Gluten-Free Pumpkin Cream Cheese Muffins are a delightful fall treat combining the warm spices of pumpkin with a creamy, tangy cream cheese swirl. Perfectly moist and tender, they use gluten-free flour and coconut sugar to create a healthier muffin that’s great for those avoiding gluten but still craving a comforting baked good.
Ingredients
Dry Ingredients
- 1 1/2 cups gluten-free all-purpose flour (ensure it contains xanthan gum)
- 1/2 cup coconut sugar (or regular sugar)
- 1 teaspoon baking soda
- 1/2 teaspoon baking powder
- 1 teaspoon ground cinnamon
- 1/2 teaspoon ground nutmeg
- 1/4 teaspoon ground ginger
- 1/4 teaspoon salt
Wet Ingredients
- 2 large eggs
- 1 cup canned pumpkin puree
- 1/2 cup unsweetened applesauce (or vegetable oil)
- 1 teaspoon vanilla extract
Cream Cheese Swirl
- 8 oz cream cheese, softened
- 1/4 cup powdered sugar
- 1 teaspoon vanilla extract
Instructions
- Preheat: Preheat the oven to 350°F (175°C). Line a muffin tin with paper liners or grease it with non-stick spray to prepare for baking.
- Mix dry ingredients: In a large mixing bowl, whisk together the gluten-free flour, coconut sugar, baking soda, baking powder, cinnamon, nutmeg, ginger, and salt until well combined to ensure even distribution of leavening and spices.
- Mix wet ingredients: In a separate bowl, beat the eggs, pumpkin puree, unsweetened applesauce, and vanilla extract until smooth and well combined, creating a cohesive wet mixture.
- Combine: Gradually add the wet ingredients to the dry ingredients. Stir gently until just combined, being careful not to overmix. The batter should be thick but uniform in consistency.
- Prepare cream cheese swirl: In a small bowl, mix the softened cream cheese, powdered sugar, and vanilla extract until smooth and creamy, ensuring no lumps remain.
- Assemble muffins: Spoon approximately 2 tablespoons of the pumpkin batter into each muffin cup. Add 1 teaspoon of the cream cheese mixture on top of the batter. Then, add a little more batter to fill each muffin cup about three-quarters full. Use a toothpick or skewer to gently swirl the cream cheese into the pumpkin batter, creating a marbled effect.
- Bake: Place the muffin tin in the preheated oven and bake for 18-22 minutes, or until a toothpick inserted in the center of a muffin comes out clean or with just a few moist crumbs.
- Cool: Allow the muffins to cool in the tin for 5 minutes to set, then transfer them to a wire rack to cool completely before serving to ensure the best texture and flavor.
Notes
- Ensure your gluten-free flour blend contains xanthan gum for proper texture and binding.
- You can substitute coconut sugar with regular granulated sugar if preferred.
- Unsweetened applesauce can be replaced with vegetable oil for a richer muffin.
- Do not overmix the batter to keep the muffins tender and moist.
- Swirling the cream cheese into the batter adds a beautiful marbled appearance and a tangy flavor contrast.
- Store leftover muffins in an airtight container at room temperature for up to 3 days, or refrigerate for up to a week.

