Gluten-free pumpkin cream cheese muffins are my idea of fall comfort. They’re soft, warmly spiced, and filled with a creamy surprise in the center. The first time I made them, the whole kitchen smelled like cinnamon and pumpkin pie; it felt like home.
These muffins were inspired by weekend baking with my mom, when we’d mix pumpkin puree and brown sugar until the spoon felt heavy. Years later, I wanted that same cozy flavor without the gluten, and this recipe did it.
They’re easy, reliable, and taste like something straight from a bakery case. Every bite is moist, sweet, and just the right amount of tangy from the cream cheese filling.
Ingredients needed for making these gluten-free pumpkin cream cheese muffins
Streusel topping:
- Gluten-free flour blend
- Sugar
- Xanthan gum
- Butter
- Pumpkin seeds
Cream cheese filling:
- Cream cheese
- Granulated sugar
- Vanilla bean paste
Pumpkin muffins:
- Pumpkin puree
- Brown soft sugar
- Sunflower oil, or another neutral-tasting oil of your choice
- Eggs
- Vanilla bean paste
- Gluten-free flour blend
- Baking powder
- Baking soda
- Xanthan gum
- Salt
- Ground cinnamon
- Ground ginger
- Ground nutmeg
- Ground allspice
How to Make Gluten-Free Pumpkin Cream Cheese Muffins (Step-by-Step)
Making these gluten-free pumpkin cream cheese muffins is easier than it looks. You’ll be mixing, layering, and baking your way to tender, golden perfection in no time.
Start with the streusel topping.
In a bowl, combine gluten-free flour, brown sugar, and a little xanthan gum. Rub in cold cubes of butter until the mix turns crumbly and clumps when pressed. Stir in pumpkin seeds for crunch, then set aside.
Make the cream cheese filling.
In a separate bowl, beat the cream cheese, sugar, and vanilla together until smooth and creamy. Spoon it into a piping bag or a small plastic bag with the tip snipped off—this makes filling the muffins clean and easy.
Mix the muffin batter.
Whisk together the pumpkin puree, sugar, oil, eggs, and vanilla until the mixture is silky smooth. In a second bowl, whisk your dry ingredients, gluten-free flour, baking powder, soda, spices, and salt. Combine wet and dry, stirring until no streaks of flour remain.
Fill and bake.
Spoon the batter into a lined muffin tin, almost to the top. Push the piping bag into the center of each muffin and squeeze a bit of cream cheese filling inside, then leave a small dollop on top. Sprinkle each muffin generously with the streusel mixture.
Bake at 375ºF (190ºC) for 25–28 minutes, until golden and firm. Let them cool for a few minutes before transferring to a rack.
Top Tips for Making Gluten-Free Pumpkin Cream Cheese Muffins
The secret to amazing gluten-free pumpkin cream cheese muffins is all in the details. These simple tips will help you get that perfect balance of soft crumb, creamy center, and golden top every time.
Use a reliable gluten-free flour blend.
Not all blends behave the same. Choose one that already contains xanthan gum or add ¼ teaspoon per cup if yours doesn’t. This helps the batter hold together, giving your muffins a tender, bakery-style texture.
Don’t overmix the batter.
Once the dry ingredients meet the wet, stir gently until no flour streaks remain. Overmixing can make gluten-free muffins dense instead of light.
Keep your ingredients at room temperature.
Soft cream cheese and room-temperature eggs help the batter mix smoothly and bake evenly. Cold ingredients can make the muffins rise unevenly.
Use real pumpkin puree.
Canned pumpkin puree, not pumpkin pie filling, is what gives these muffins their rich flavor and deep color. It also keeps them naturally moist without needing extra butter.
Bake at the right temperature.
A hot oven (375°F) helps the muffins lift quickly and stay fluffy. Too low, and the cream cheese may sink; too high, and the tops brown too fast.
Don’t skip the cooling time.
Let muffins rest for at least ten minutes before removing them from the pan. The centers finish setting during this time, locking in that creamy filling.
How to Store Gluten-Free Pumpkin Cream Cheese Muffins
Store the gluten-free pumpkin cream cheese muffins in an airtight container in the refrigerator for 3–4 days.
More gluten-free desserts to make ASAP!
- Soft & Fluffy Gluten-Free Cinnamon Rolls
- Gluten-Free Black Forest Gateau – Rich, Chocolatey & Delicious
- Gluten-Free Churros (Crispy, Cinnamon-Sugar)
- Gluten Free Blueberry Streusel Muffins (Bakery-Style)
- Gluten Free Blueberry Crumb Cake
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Gluten-Free Pumpkin Cream Cheese Muffins
Gluten-free pumpkin cream cheese muffins that are soft, spiced, and filled with creamy centers, perfect for cozy fall mornings.
Ingredients
Streusel topping:
- ⅔ cup plain gluten-free flour blend
- 3 tbsp light brown soft sugar
- ¼ tsp xanthan gum
- 3 tbsp cold unsalted butter, cubed
- ⅓ cup pumpkin seeds
Cream cheese filling:
- 1 cup full-fat cream cheese, room temperature
- ¼ cup caster/superfine or granulated sugar
- ½ teaspoon vanilla bean paste (or 1 teaspoon vanilla extract)
Pumpkin muffins:
- 1¾ cups canned pumpkin puree
- 1 cup light brown soft sugar
- ½ cup sunflower oil, or another neutral-tasting oil of your choice
- 2 large eggs, room temperature
- ½ teaspoon vanilla bean paste (or 1 teaspoon vanilla extract)
- 2 cups plain gluten-free flour blend
- 2 tsp baking powder
- 1 tsp baking soda
- ½ tsp xanthan gum
- ¼ tsp salt
- 2 tsp ground cinnamon
- 1 tsp ground ginger
- ½ tsp ground nutmeg
- ½ tsp ground allspice
Instructions
- In a bowl, combine gluten-free flour, brown sugar, and a little xanthan gum.
- Rub in cold cubes of butter until the mix turns crumbly and clumps when pressed.
- Stir in pumpkin seeds for crunch, then set aside.
- In a separate bowl, beat the cream cheese, sugar, and vanilla together until smooth and creamy.
- Spoon it into a piping bag or a small plastic bag with the tip snipped off—this makes filling the muffins clean and easy.
- Whisk together the pumpkin puree, sugar, oil, eggs, and vanilla until the mixture is silky smooth.
- In a second bowl, whisk your dry ingredients, gluten-free flour, baking powder, soda, spices, and salt.
- Combine wet and dry, stirring until no streaks of flour remain.
- Spoon the batter into a lined muffin tin, almost to the top.
- Push the piping bag into the center of each muffin and squeeze a bit of cream cheese filling inside, then leave a small dollop on top.
- Sprinkle each muffin generously with the streusel mixture.
- Bake at 375ºF (190ºC) for 25–28 minutes, until golden and firm.
- Let them cool for a few minutes before transferring to a rack.
