Gluten-Free Blueberry Cream Cheese Muffins
Soft, fluffy gluten-free blueberry muffins with a sweetened cream cheese layer on top that melts into a creamy, cheesecake-like finish. Loaded with fresh blueberries and sprinkled with crunchy turbinado sugar before baking.
- Prep10 min
- Cook18 min
- Total28 min
- Yield12 muffins
25 Jul 2011

These gluten-free blueberry cream cheese muffins are soft, tender, and absolutely loaded with juicy blueberries. The sweetened cream cheese on top bakes down into this rich, almost cheesecake-like layer that honestly makes them just as good for dessert as they are for breakfast.
The batter is oil-based, so there’s no waiting around for butter to soften, and the cream cheese filling is just three ingredients. You toss the blueberries in a little flour to keep them from sinking, spoon on the cream cheese mixture, and that’s it. Gluten-free, easy to make dairy-free, and they never last long around here.

Ingredient Notes
- Cream Cheese – Full-fat, block-style, softened to room temperature. This matters more than you’d think. Cold cream cheese leaves lumps in the filling, and those lumps don’t magically smooth out in the oven.
- Gluten-Free Flour Blend – I’ve tested this with Bob’s Red Mill 1-to-1 (blue bag) and King Arthur Gluten-Free All-Purpose. Both work great. I can’t guarantee results with other brands.
- Vegetable Oil – Any neutral oil works: vegetable, canola, avocado.
- Blueberries – Fresh gives you the best texture and the least color bleeding. Frozen works too, but keep them frozen when you toss them in flour and fold them in. Don’t thaw them first or you’ll end up with purple batter.
- Turbinado Sugar – This is what gives the muffins that crackly, sparkly top. Regular granulated sugar won’t give you the same crunch. Look for it near the regular sugar; it’s sometimes labeled “raw sugar.”
How to Quickly Soften Cream Cheese
Leave the cream cheese in the foil packaging and place it in a bowl of warm water (not hot water) for about 5 minutes. It will soften to room temperature without melting. Always use room temperature cream cheese for a smooth filling.
Expert Tips
- Toss blueberries in flour before folding them in. Reserve 1 tablespoon of gluten-free flour from the recipe to coat the blueberries. This helps them stay suspended in the batter instead of sinking to the bottom.
- Use a cookie scoop for even muffins. A large cookie scoop (about 3 tablespoons) fills each cup to the right level and keeps all 12 muffins the same size so they bake evenly.
Storage Instructions
Room Temperature: Store in an airtight container for up to 2 days. The cream cheese topping means they shouldn’t sit out longer than that.
Refrigerate: Wrap individually or store in a sealed container for up to 5 days. Bring to room temperature before eating, or warm in the microwave for 15-20 seconds.
Freeze: Freeze muffins in a single layer on a baking sheet until solid, then transfer to a freezer bag. They keep for up to 3 months. Thaw overnight in the refrigerator or microwave from frozen for 30-40 seconds.
Serving Suggestions
Set out a batch of these alongside gluten-free chocolate muffins and gluten-free lemon poppy seed muffins for a brunch muffin spread. They also pair well with a gluten-free blueberry banana bread for a blueberry-themed breakfast. For a lighter option, serve them with fresh fruit and yogurt.
Method
-
1
Preheat oven to 400°F. Line a 12-cup muffin tin with paper baking cups.
-
2
To make cream cheese mixture, beat 4 oz cream cheese, ¼ cup granulated sugar, and ½ teaspoon pure vanilla extract with a hand mixer until smooth and creamy. Set aside.
-
3
Set aside 1 tablespoon of the 2 cups gluten-free all-purpose flour blend to toss with the blueberries later.
-
4
In another bowl, whisk together the remaining gluten-free flour blend, 2 teaspoons baking powder, ½ teaspoon baking soda, ½ teaspoon ground cinnamon and ½ teaspoon salt. Set aside.
-
5
In a large bowl, mix together ¾ cup granulated sugar and ½ cup vegetable oil for 2 minutes.
-
6
Then, add 2 large eggs to the sugar mixture and beat until combined and smooth, about 1-2 minutes.
-
7
Add ¾ cup whole milk and 1 teaspoon vanilla extract into the mixture and mix well until combined.
-
8
Gradually add flour mixture to wet ingredients, mixing until just combined.
-
9
Toss 1 cups blueberries with the reserved 1 tablespoon of gluten-free flour until coated. This will help them from sinking to the bottom of the muffins.
-
10
Gently fold coated blueberries into batter, being careful not to crush them.
-
11
Scoop batter into prepared muffin cups, filling each about three-quarters full. Press remaining 0.25 cups blueberries into tops of batter.
-
12
Spoon a heaping teaspoon of cream cheese topping onto each muffin. Sprinkle 2 teaspoons turbinado sugar over tops.
-
13
Bake at 400°F for 16-18 minutes, until muffins are lightly golden and a toothpick inserted into the center (avoiding cream cheese layer) comes out clean.
-
14
Let cool in pan for 5 minutes before transferring to a wire rack. Serve warm or at room temperature.
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