These Gluten-Free Pumpkin Cream Cheese Muffins Recipe are an absolute game-changer when it comes to cozy fall baking. Imagine tender, moist pumpkin muffins infused with warming spices, perfectly complemented by a luscious swirl of tangy cream cheese. Whether you’re gluten intolerant or just craving a delicious autumn treat, this recipe combines simple ingredients into a show-stopping bake that’s both comforting and indulgent. With every bite, you’ll get the perfect balance of pumpkin richness and creamy sweetness, making these muffins impossible to resist.

Ingredients You’ll Need
This Gluten-Free Pumpkin Cream Cheese Muffins Recipe uses a handful of straightforward yet essential ingredients that deliver incredible flavor, moist texture, and that inviting fall color we all love. Each component plays a crucial role, from the gluten-free flour for structure to the warm spices that elevate the pumpkin’s natural sweetness.
- 1 1/2 cups gluten-free all-purpose flour: Make sure it includes xanthan gum for the perfect muffin crumb and texture.
- 1/2 cup coconut sugar: Adds a subtle caramel flavor while keeping sweetness natural; you can substitute with regular sugar if preferred.
- 1 teaspoon baking soda: Essential for leavening and light, fluffy muffins.
- 1/2 teaspoon baking powder: Works alongside baking soda to ensure the muffins rise perfectly.
- 1 teaspoon ground cinnamon: Brings that iconic warm fall spice that pumpkin always calls for.
- 1/2 teaspoon ground nutmeg: Adds depth and a slight nutty aroma to the spice blend.
- 1/4 teaspoon ground ginger: A gentle kick of spice that complements the sweetness beautifully.
- 1/4 teaspoon salt: Enhances all the flavors, balancing the sweet and savory.
- 2 large eggs: Bind ingredients together and enrich the batter.
- 1 cup canned pumpkin puree: The star ingredient, providing moisture, flavor, and that gorgeous orange hue.
- 1/2 cup unsweetened applesauce: Adds moistness and tenderness; vegetable oil can be used as an alternative for richer muffins.
- 1 teaspoon vanilla extract: Amplifies the sweetness and rounds out the pumpkin flavor.
- 8 oz cream cheese, softened: The creamy, tangy swirl that sets these muffins apart.
- 1/4 cup powdered sugar: Sweetens and smooths the cream cheese mixture perfectly.
- 1 teaspoon vanilla extract: Mixed into the cream cheese for a deliciously fragrant finish.
How to Make Gluten-Free Pumpkin Cream Cheese Muffins Recipe
Step 1: Preheat and Prepare Your Muffin Tin
Start by preheating your oven to 350°F (175°C). This ensures the oven is at the perfect temperature when your batter is ready. Line your muffin tin with paper liners or lightly grease it with non-stick spray to make removal easy later on.
Step 2: Mix the Dry Ingredients
In a large mixing bowl, whisk together the gluten-free all-purpose flour, coconut sugar, baking soda, baking powder, cinnamon, nutmeg, ginger, and salt. Combining these dry ingredients first ensures that every spice and leavening agent is evenly distributed throughout the batter, which is key to uniform muffins.
Step 3: Combine the Wet Ingredients
In a separate bowl, beat the eggs with pumpkin puree, unsweetened applesauce, and vanilla extract until the mixture is smooth and homogenous. This blend not only provides moisture and flavor but also helps create the tender texture we want in our muffins.
Step 4: Bring Wet and Dry Ingredients Together
Gradually add the wet ingredients into the bowl with the dry ingredients, mixing gently until just combined. Be careful not to overmix; the batter will be thick but that’s exactly how it should be to give your muffins their perfect structure.
Step 5: Prepare the Cream Cheese Swirl
In a small bowl, mix the softened cream cheese with powdered sugar and vanilla extract until the mixture is smooth and creamy. This swirl will add an irresistible tang and silky texture to every muffin bite.
Step 6: Assemble the Muffins
Start by spooning about 2 tablespoons of the muffin batter into each muffin cup. Then add a teaspoon of the cream cheese mixture on top. Cover with additional batter to fill the cups about three-quarters full. Use a toothpick or skewer to swirl the cream cheese gently into the muffin batter, creating a beautiful marbled effect.
Step 7: Bake and Cool
Bake your muffins for 18-22 minutes. You’ll know they’re done when a toothpick inserted into the center comes out clean. Allow the muffins to cool in the tin for 5 minutes before transferring them to a wire rack to cool completely. This prevents them from becoming soggy and keeps their delicate crumb intact.
How to Serve Gluten-Free Pumpkin Cream Cheese Muffins Recipe

Garnishes
These muffins shine on their own, but a light dusting of powdered sugar or a sprinkle of cinnamon on top can make them feel extra special if you’re hosting or just feeling fancy. A small dollop of whipped cream or a drizzle of honey works beautifully for an added touch of sweetness and moisture.
Side Dishes
Serve these muffins alongside a steaming mug of chai tea, spiced coffee, or hot apple cider to truly capture the cozy fall vibe. They also pair well with simple fresh fruit like sliced apples or pears, which complement the warm spices perfectly and add a refreshing balance.
Creative Ways to Present
For a festive breakfast or brunch, arrange your Gluten-Free Pumpkin Cream Cheese Muffins Recipe on a decorative platter with small bowls of cream cheese frosting, maple syrup, or even nut butter for dipping. They can also be split open and lightly toasted for a warm, melty cream cheese treat that’s sure to impress your guests.
Make Ahead and Storage
Storing Leftovers
Once completely cooled, store your muffins in an airtight container at room temperature for up to three days. This keeps them moist and delicious without drying out.
Freezing
These muffins freeze wonderfully! Wrap each muffin individually in plastic wrap or foil, then place them in a freezer bag. They’ll keep well for up to three months, making them a perfect make-ahead treat for busy mornings.
Reheating
To reheat, simply thaw your muffin at room temperature or warm it gently in a microwave for 20-30 seconds. For a crispier top, pop the muffin into a toaster oven for a couple of minutes. It’s like enjoying them fresh out of the oven all over again!
FAQs
Can I substitute the pumpkin puree with fresh pumpkin?
Yes, you can use fresh pumpkin, but make sure to cook and puree it thoroughly until smooth. Fresh pumpkin can have more moisture, so you may need to adjust the wet ingredients slightly to keep the batter from becoming too runny.
Is it possible to make these muffins dairy-free?
Absolutely! You can substitute the cream cheese with a dairy-free cream cheese alternative and use a dairy-free milk or oil in place of applesauce for moistness. Just keep an eye on the texture and adjust if needed for best results.
What if I don’t have coconut sugar? Can I use regular sugar instead?
Regular granulated sugar is a fine substitute if you don’t have coconut sugar. It won’t significantly change the taste, though coconut sugar adds a subtle caramel note that pairs beautifully with pumpkin.
How can I make sure my muffins don’t fall apart without gluten?
The key is using a gluten-free flour blend that contains xanthan gum or another binding agent, which mimics gluten’s elasticity. Be sure not to overmix your batter to keep the texture light and tender, preventing crumbliness.
Can I double this recipe for a larger batch?
Definitely! Just double all ingredients and bake in two muffin tins or in batches. Keep the baking time about the same, but check for doneness with a toothpick since ovens can vary.
Final Thoughts
There’s something truly magical about a muffin that can satisfy a seasonal craving while being gluten-free and packed with flavor. This Gluten-Free Pumpkin Cream Cheese Muffins Recipe offers exactly that—a tender, moist bite of pumpkin perfection topped with a creamy swirl that feels like a warm hug on an autumn day. I encourage you to dive into this recipe, enjoy every step, and share these delightful muffins with your loved ones. Once you try them, I’m confident they’ll become a beloved staple in your baking repertoire.
Print
Gluten-Free Pumpkin Cream Cheese Muffins Recipe
- Prep Time: 10 minutes
- Cook Time: 20 minutes
- Total Time: 30 minutes
- Yield: 12 servings
- Category: Baking
- Method: Baking
- Cuisine: American
- Diet: Gluten Free
Description
Delight in these moist and flavorful Gluten-Free Pumpkin Cream Cheese Muffins, perfect for fall or any time you crave a tender, spiced treat. Featuring a rich pumpkin base combined with a creamy, sweetened cream cheese swirl, these muffins are both gluten-free and irresistibly delicious.
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 oven: Preheat your oven to 350°F (175°C). Line a muffin tin with paper liners or grease it with non-stick spray to prevent sticking.
- Mix dry ingredients: In a large mixing bowl, whisk together the gluten-free all-purpose flour, coconut sugar, baking soda, baking powder, ground cinnamon, ground nutmeg, ground ginger, and salt, ensuring a uniform mixture.
- Mix wet ingredients: In a separate bowl, beat the eggs, pumpkin puree, unsweetened applesauce (or vegetable oil), and vanilla extract until smooth and well combined to create a moist pumpkin base.
- Combine wet and dry: Gradually add the wet ingredients to the dry ingredients, mixing just until combined. The batter will be thick—avoid overmixing to keep muffins tender.
- Prepare cream cheese swirl: In a small bowl, mix the softened cream cheese with powdered sugar and vanilla extract until smooth and creamy, perfect for swirling into the muffins.
- Assemble muffins: Spoon about 2 tablespoons of muffin batter into each muffin cup. Add 1 teaspoon of the cream cheese mixture on top, then cover with more muffin batter to fill each cup about 3/4 full. Use a toothpick to gently swirl the cream cheese into the pumpkin batter for a marbled effect.
- Bake: Bake in the preheated oven for 18-22 minutes, or until a toothpick inserted into the center comes out clean. This ensures the muffins are fully cooked but still moist.
- Cool: Allow the muffins to cool in the tin for 5 minutes before transferring them to a wire rack to cool completely, enhancing texture and flavor.
Notes
- Ensure your gluten-free flour blend contains xanthan gum for proper texture and structure.
- You can substitute coconut sugar with regular granulated sugar or brown sugar if preferred.
- Applesauce can be replaced with an equal amount of vegetable oil for a richer texture.
- For a dairy-free version, use vegan cream cheese alternatives.
- Muffins can be stored in an airtight container at room temperature for up to 3 days or refrigerated for up to a week.
- Freeze muffins for up to 3 months; thaw before serving.

