These gluten-free pumpkin cream cheese muffins are the perfect cozy fall bake, with a soft and tender pumpkin muffin wrapped around a rich, cream cheese center. Warm cinnamon and pumpkin pie spices give the muffins plenty of classic fall flavor, while the tangy cream cheese filling makes every bite feel a little extra special.

They’re easy enough for a weekend breakfast but just indulgent enough to feel like a bakery-style treat. Pair one with a hot cup of coffee for a cozy fall morning, or make a batch to have on hand for an easy seasonal snack.

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Why You’ll Love This Recipe

Soft and moist 
Pumpkin puree, brown sugar, and oil give these muffins a wonderfully soft, moist texture that stays tender even after they cool.

Creamy cheesecake filling 
Each muffin is topped with a rich cream cheese filling that sinks slightly into the center as it bakes, giving you a little cheesecake in every bite.

Warmly spiced 
Pumpkin pie spice and cinnamon add plenty of cozy fall flavor without overpowering the pumpkin. 

Perfect for fall 
With pumpkin, warm spices, and a creamy filling, these muffins make a cozy addition to fall breakfasts, brunches, or afternoon coffee breaks.

Easy to make 
There’s no complicated layering or filling after baking—the cream cheese mixture is piped right onto the muffin batter before the pan goes into the oven.

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Ingredient Notes

Gluten-free 1:1 flour 
A gluten-free 1:1 baking flour gives the muffins structure while keeping the recipe completely gluten-free. I recommend using a blend that contains xanthan gum.

Almond flour 
A small amount of finely ground blanched almond flour helps give the muffins a soft, tender crumb. The recipe uses just ¼ cup alongside the gluten-free 1:1 flour. 

Pumpkin puree 
Be sure to use 100% pure canned pumpkin puree rather than pumpkin pie filling, which contains added sugar and spices. Bring the pumpkin to room temperature before mixing the batter.

Pumpkin pie spice + cinnamon 
Using both gives the muffins their warm, cozy flavor. The additional cinnamon enhances the spice blend without making the muffins overly spiced.

Granulated + light brown sugar 
Granulated sugar provides sweetness, while light brown sugar adds a subtle caramel-like flavor and additional moisture.

Avocado oil 
Oil keeps the pumpkin muffins especially soft and moist. You can substitute another neutral-flavored baking oil if preferred. 

Cream cheese 
Use full-fat, block-style cream cheese rather than the spreadable kind sold in a tub. Let it come to room temperature so the filling mixes up smooth and creamy. 

Milk 
A tablespoon of whole milk loosens the cream cheese mixture just enough to give it a smooth, pipeable consistency.

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How to Make Gluten-Free Pumpkin Cream Cheese Muffins

See the recipe card below for the full ingredient list, measurements, and instructions.

Step 1: Make the cream cheese filling
Beat the cream cheese, sugar, milk, gluten-free flour, vanilla, and salt together until smooth and fluffy. Transfer the filling to a piping bag fitted with a large round tip and set aside.

Step 2: Whisk the wet ingredients
Whisk the pumpkin puree, granulated sugar, brown sugar, eggs, oil, and vanilla until smooth.

Step 3: Add the dry ingredients
Whisk the gluten-free 1:1 flour, almond flour, baking powder, baking soda, salt, pumpkin pie spice, and cinnamon together in a medium bowl. Add the dry ingredients to the wet ingredients and gently fold together with a rubber spatula just until no streaks of flour remain.

Step 4: Fill the muffin pan
Divide the batter evenly between 12 lined muffin cups, filling each about 3/4 full.

Step 5: Add the cream cheese filling and bake
Pipe about 1 tablespoon of cream cheese filling onto the center of each muffin, inserting the piping tip just slightly into the batter before lifting upward. Bake at 350°F (177°C) for 18–24 minutes, then allow the muffins to cool in the pan for about 15 minutes before transferring them to a wire rack.

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Recipe Tips

Use room temperature ingredients
Bring the cream cheese, milk, pumpkin puree, and eggs to room temperature before getting started. This helps everything combine more smoothly, especially the cream cheese filling. 

Use block-style cream cheese
For the thickest, creamiest filling, use full-fat block-style cream cheese rather than cream cheese from a tub. 

Don’t overmix the batter
Once you add the dry ingredients, gently fold everything together just until no streaks of flour remain. A few small lumps are perfectly fine and will help keep the muffins soft and tender. 

Don’t overfill the muffin liners
Fill each liner about ¾ full to leave enough room for the muffins to rise and for the cream cheese topping. The recipe should make 12 muffins. 

Don’t use too much cream cheese filling
About 1 tablespoon of cream cheese filling per muffin is plenty. Using too much can cause the filling to sink too far into the muffin as it bakes and cools. 

Pipe the filling just into the surface of the batter
Insert the piping tip only slightly into the center of the muffin batter, then pipe while slowly lifting the bag upward before finishing with a swirl on top. The cream cheese will naturally sink a little as the muffins bake. 

Let the muffins cool before removing them
Allow the muffins to cool in the pan for about 15 minutes before transferring them to a wire rack. This gives the freshly baked muffins a little time to set before you move them.

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Storage 

Refrigerator
Because these muffins contain a cream cheese filling, I recommend storing them in an airtight container in the refrigerator. They should keep well for about 4–5 days. For the best texture, let a muffin sit at room temperature for about 15–20 minutes before serving.

Freezer
The muffins can also be frozen. Once completely cooled, place them in an airtight freezer-safe container or individually wrap them before freezing for up to 2 months. Thaw overnight in the refrigerator, then bring to room temperature before serving.

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Frequently Asked Questions

Can I use pumpkin pie filling instead of pumpkin puree?
No. Be sure to use 100% pure pumpkin puree for this recipe. Pumpkin pie filling contains added sugar and spices and will change the flavor and sweetness of the muffins.

Why did my cream cheese filling sink into the muffins?
The cream cheese will naturally sink slightly as the muffins bake and cool. To keep most of the filling visible on top, use about 1 tablespoon per muffin and insert the piping tip only slightly into the batter before piping upward and finishing with a swirl. 

Can I use spreadable cream cheese?
I recommend using full-fat, block-style cream cheese. Spreadable cream cheese has a different consistency and may result in a softer filling that doesn’t hold its shape as well.

Can I make these muffins ahead of time?
Yes! These muffins can be made a day or two in advance and stored in an airtight container in the refrigerator. Let them sit at room temperature for about 15–20 minutes before serving for a softer texture.

How do I know when the muffins are done?
The muffins are ready when they have risen and the pumpkin portion springs back lightly when touched. Because of the cream cheese center, insert a toothpick into the pumpkin muffin portion rather than directly through the cream cheese when checking for doneness. The recipe calls for approximately 18–24 minutes at 350°F.

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Photography by Creating Kaitlin

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