Easy Gluten-Free Strawberry Muffins with Cream Cheese
These Gluten-Free Strawberry Muffins with a Cream Cheese Filling are made with almond flour, cassava flour, cottage cheese, applesauce, eggs, and fresh strawberries. Topped with a sweet crumble of toasted almonds and strawberries, they’re perfect for breakfast or special occasions like Mother’s Day, brunches, and Easter.

These Gluten-Free Strawberry Muffins with a Cream Cheese Filling are the perfect treat for breakfast or an afternoon snack. Made with wholesome ingredients like almond flour, cassava flour, cottage cheese, unsweetened applesauce, and fresh strawberries, these muffins are packed with flavor and texture. The sweet crumble on top, featuring toasted almonds and juicy strawberries, adds an extra touch of deliciousness.
This recipe is a great way to celebrate strawberry season, and it’s perfect for making ahead of time for busy mornings. They not only taste amazing but also look like they came straight from a bakery, making them an impressive option for serving at special occasions like Mother’s Day, brunches, showers, or Easter. Whether you’re a seasoned baker or it’s your first time, these muffins will quickly become a favorite in your kitchen.
Why You’ll Love This Easy Strawberry Muffin Recipe
- Gluten-free and flavorful: Made with almond and cassava flour for a tasty, gluten-free treat.
- Creamy filling: Each muffin is filled with a delicious cream cheese center that pairs perfectly with fresh strawberries.
- Perfect for special occasions: These muffins look bakery-worthy and are ideal for Mother’s Day or brunches.
- Make-ahead convenience: Great for busy mornings or prepping ahead for gatherings.

Ingredients & Substitutions
Here is everything you need to make the best-tasting cream cheese filled strawberry muffins recipe:
Cottage Cheese: Consider using sour cream, Greek yogurt, ricotta cheese, or plant-based yogurt for a dairy-free option.
Avocado Oil: Opt for light olive oil, melted coconut oil, melted butter, or any neutral-flavored vegetable oil.
Unsweetened Applesauce: Try substituting with mashed banana, pureed pumpkin, or plain yogurt.
Cane Sugar: You can use any granular sugar, including brown sugar or pure maple syrup (reduce liquid slightly if using).
Vanilla Extract: Swap out for almond extract (use 1/2 teaspoon as it is stronger), or 1 vanilla bean (seeds scraped).
Large Eggs: Use 2 flax eggs (2 tablespoons ground flaxseed mixed with 6 tablespoons water, let sit for 5 minutes), or 1/2 cup mashed banana or applesauce (for binding but will change texture slightly).
Cassava Flour: Substitute with tapioca flour or arrowroot flour (use less, about 3/4 cup), or a gluten-free all-purpose flour blend. You may need to adjust the amount to get the same consistency.
Almond Flour: Switch to hazelnut flour, sunflower seed flour, or a gluten-free all-purpose flour blend. You may need to adjust the amount to get the same consistency.
Cinnamon: Try using pumpkin pie spice, allspice, or cardamom.
Nutmeg: Go for allspice or mace.
Fresh Strawberries: You can substitute the strawberries with fresh berries, including chopped raspberries, blueberries, or finely chopped apples. For best results, use ripe sweet strawberries.
Cream Cheese: Choose Neufchâtel cheese, mascarpone, or a dairy-free cream cheese alternative.
Egg Yolk: Substitute with 1 tablespoon Greek yogurt, 1 tablespoon unsweetened applesauce, or 1 tablespoon of any nut or seed butter for binding.
Vanilla Extract: Use almond extract (use 1/4 teaspoon), or 1/2 vanilla bean (seeds scraped).
Lemon Juice: Opt for lime juice, apple cider vinegar, or a splash of white vinegar.
Butter: Consider using coconut oil, vegan butter, or ghee.

How to Make My Healthy Gluten-Free Strawberry Muffins Recipe
Here are easy, detailed, step-by-step instructions for making this gluten-free muffin recipe. The instructions are also repeated in the recipe card at the bottom of this blog post.
Step 1: Prepare the Cream Cheese Filling
In a medium bowl, beat together the cream cheese, egg yolk, vanilla extract, lemon juice, and cane sugar until smooth and creamy. Set aside.

Step 2: Make the Muffin Batter
Preheat the oven to 350°F (175°C). Line a muffin tin with paper liners or lightly grease with oil or non-stick spray.
If using cottage cheese, blend it smooth in a food processor, blender or chopper cup with an immersion blender.
In a large mixing bowl, combine the eggs, cottage cheese, avocado oil, and unsweetened applesauce, cane sugar and vanilla extract and mix until well combined.
Add the dry ingredients, including cassava flour, almond flour, baking powder, cinnamon, and nutmeg and mix until just combined.
Fold in the chopped strawberries gently with a spatula to avoid over-mixing.


Step 3: Prepare the Crumble Topping
In a small bowl, combine the almond flour, cassava flour, butter, sugar, and salt. Mix with your fingers or a fork until the mixture resembles coarse crumbs.

Step 4: Fill the Muffin Cups
Spoon a heaping tablespoon of muffin batter into each muffin cup, filling them about halfway using an ice cream scoop or batter scoop.
Add a dollop of the cream cheese filling on top of the batter in each cup.
Spoon the remaining muffin batter over the cream cheese filling, ensuring each muffin cup is about 3/4 full.
Sprinkle the crumble evenly over the tops of the muffins. Then add more chopped strawberries and toasted almonds and sprinkle coarse sea salt on top of each muffin.


Step 5: Bake the Muffins
Place the muffin tin in the preheated oven and bake for 25-28 minutes, or until a toothpick inserted into the center of a muffin comes out clean (avoid the cream cheese filling when testing).
Allow the muffins to cool in the tin for about 5 minutes, then transfer them to a cooling rack to cool completely.

Expert Recipe Tips
Choosing Strawberries: For the best flavor, use fresh, ripe strawberries. If using frozen strawberries, make sure to thaw and drain them well to avoid excess moisture in the batter. You can also make blueberry muffins, swapping the strawberries for blueberries.
Mixing the Batter: Avoid over-mixing the batter once you add the dry ingredients. Over-mixing can lead to dense muffins. Mix until just combined for the best texture.
Filling the Muffin Cups: To ensure an even distribution of the cream cheese filling, use a small spoon or a piping bag to add the filling to the center of each muffin cup.
Testing for Doneness: When checking if the muffins are done, be careful to insert the toothpick into the muffin batter and not the cream cheese filling. The filling will remain soft even when the muffins are fully baked.
Do you love muffins? Check out more of my easy and nutritious muffin recipes:

Easy Gluten-Free Strawberry Muffins with Cream Cheese

Ingredients
- 1/4 cup cottage cheese (or sour cream)
- 1/4 cup avocado oil (or light olive oil)
- 1/4 cup unsweetened applesauce
- 1/3 cup cane sugar
- 2 teaspoons vanilla extract
- 2 eggs
- 1 cup cassava flour
- 1 cup almond flour
- 2 teaspoons baking powder
- 1/2 teaspoon cinnamon
- 1/4 teaspoon nutmeg
- 1 cup chopped strawberries
Cream Cheese Filling:
- 6 ounces cream cheese
- 1 egg yolk
- 1 teaspoon vanilla extract
- 1 teaspoon lemon juice
- 3 tablespoons cane sugar
Crumble:
- 1/4 cup almond flour
- 1/4 cup cassava flour
- 2 tablespoons butter
- 2 tablespoons sugar
Instructions
- Make the Cream Cheese Filling: In a medium bowl, beat together the cream cheese, egg yolk, vanilla extract, lemon juice, and cane sugar until smooth and creamy. Set aside.
- Make the Muffin Batter: Preheat the oven to 350°F (175°C). Line a muffin tin with paper liners or lightly grease with oil or non-stick spray.If using cottage cheese, blend it smooth in a food processor, blender or chopper cup with an immersion blender.In a large mixing bowl, combine the eggs, cottage cheese, avocado oil, and unsweetened applesauce, cane sugar and vanilla extract and mix until well combined.Add the dry ingredients, including cassava flour, almond flour, baking powder, cinnamon, and nutmeg and mix until just combined.Fold in the chopped strawberries gently with a spatula to avoid over-mixing.
- Make the Crumble Topping: In a small bowl, combine the almond flour, cassava flour, butter, sugar, and salt. Mix with your fingers or a fork until the mixture resembles coarse crumbs.
- Fill the Muffin Cups: Spoon a heaping tablespoon of muffin batter into each muffin cup, filling them about halfway.Add a dollop of the cream cheese filling on top of the batter in each cup.Spoon the remaining muffin batter over the cream cheese filling, ensuring each muffin cup is about 3/4 full.Sprinkle the crumble evenly over the tops of the muffins. Then add more chopped strawberries and toasted almonds and sprinkle coarse sea salt on top of each muffin.
- Bake the Muffins: Place the muffin tin in the preheated oven and bake for 25-28 minutes, or until a toothpick inserted into the center of a muffin comes out clean (avoid the cream cheese filling when testing).Allow the muffins to cool in the tin for about 5 minutes, then transfer them to a cooling rack to cool completely.
Video

I tried making these, and wow they are delicious! The crunchy topping mixed with the creamy filling is TO DIE FOR. I’ll be making these more often for sure!
Thank you so much for your review, Katie!!! I love that you love them as much as I do 🙂
OMGoodness…these are soooo good! The strawberry flavor is just right and the cream cheese filling is super delish. I used chopped almonds and mixed them with the crumble. Will be making these again!
You’re so welcome, Wendy! I’m so glad you love these muffins 🙂 Adding the chopped almonds to the crumble is a great idea!
I’m so excited to share this recipe with you! These muffins taste even better than they look! Please let me know how these turn out for you 🙂