Easy Gluten-Free Strawberry Muffins with Cream Cheese

This is the best-tasting recipe for gorgeous Gluten-Free Strawberry Muffins with a cream cheese filling and a simple crumble on top. These healthy strawberry muffins are gluten-free with almond flour and cassava flour and include cottage cheese, unsweetened applesauce, eggs, cinnamon, cream cheese, toasted almonds, and lemon juice. You’ll be proud to serve them for Mother’s Day, brunches, showers, Easter, or any special occasion.

Gluten-free strawberry cream cheese filled muffins with crumble topping on a cooling rack.

This is the best-tasting Gluten-Free Strawberry Muffins with a Cream Cheese Filling recipe for delicious muffins for a quick breakfast or afternoon snack. These healthy strawberry muffins are gluten-free with almond flour and cassava flour and include cottage cheese, unsweetened applesauce, eggs, cinnamon, cream cheese, toasted almonds, and lemon juice. They also have a sweet crumble on top with toasted almonds and more fresh strawberries.

This is the perfect gluten-free muffin recipe to enjoy juicy strawberries during strawberry season, even if this is your first time. You can make them ahead of time for busy mornings. They look like they came out of a bakery, so you’ll be proud to serve them for Mother’s Day, brunches, showers, Easter, or any special occasion.

YouTube video

Why You’ll Love This Easy Strawberry Muffin Recipe

  • You only need a few simple ingredients.
  • It is super easy to make for an impressive result.
  • The flavor-rich ingredients make it taste amazing!
  • All the ingredients are easily digestible for a gentle tummy.
Gluten-free strawberry cream cheese filled muffins with crumble topping on a cooling rack.

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.

Gluten-free strawberry cream cheese filled muffins with crumble topping on a cooling rack.

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.

Gluten-free strawberry cream cheese filled muffins with crumble topping on a cooling rack.

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.

Gluten-free strawberry cream cheese filled muffins with crumble topping on a cooling rack.
Gluten-free strawberry cream cheese filled muffins with crumble topping on a cooling rack.

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.

Gluten-free strawberry cream cheese filled muffins with crumble topping on a cooling rack.

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.

Gluten-free strawberry cream cheese filled muffins with crumble topping on a cooling rack.
Gluten-free strawberry cream cheese filled muffins with crumble topping on a cooling rack.

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.

Gluten-free strawberry cream cheese filled muffins with crumble topping on a cooling rack.

Helpful Recipe Notes

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.

Room Temperature: Store in an airtight container for up to 2 days.

Refrigeration: Keep in an airtight container in the fridge for up to 5 days.

Freezing: Freeze in a single layer, then transfer to a freezer bag or container. Store for up to 3 months.

Thawing: Thaw at room temperature or warm in the microwave for 20-30 seconds.

Reheating: Reheat in the microwave for 15-20 seconds or in a 350°F oven for 5-10 minutes.

Can I use frozen strawberries instead of fresh in this gluten-free strawberry muffin recipe?
Yes, you can use frozen strawberries. Make sure to thaw and drain them well to avoid excess moisture in the batter.

Can I make this gluten-free strawberry muffins recipe dairy-free?
Absolutely! Substitute plant-based yogurt for the cottage cheese, use a dairy-free cream cheese alternative for the filling, and replace the butter in the crumble with coconut oil or vegan butter.

How do I make this recipe egg-free?
To make it egg-free, use flax eggs (2 tablespoons ground flaxseed mixed with 6 tablespoons water) in place of the eggs in the batter, and 1 tablespoon of Greek yogurt or unsweetened applesauce instead of the egg yolk in the cream cheese filling.

Can I use a different type of flour in healthy almond flour muffins?
Yes, you can substitute cassava flour with tapioca flour or arrowroot flour (use less, about 3/4 cup), or a gluten-free all-purpose flour blend. Almond flour can be replaced with hazelnut flour, sunflower seed flour, or a gluten-free all-purpose flour blend.

Can I add other fruits to the delicious strawberry muffins?
Yes, you can add other fruits such as raspberries, blueberries, or finely chopped apples. 

How can I tell if the muffins are done?
Insert a toothpick into the muffin batter (not the cream cheese filling) to check for doneness. If it comes out clean or with a few crumbs, the muffins are done. Avoid testing the cream cheese filling, as it will remain soft even when the muffins are fully baked.

Can I make the crumble topping crunchier?
For a crunchier topping, you can add a tablespoon of chopped nuts or oats to the crumble mixture before sprinkling it on top of the muffins.

What if I don’t have vanilla extract?
You can substitute vanilla extract with almond extract (use 1/2 teaspoon as it is stronger), or scrape the seeds from 1 vanilla bean.

Gluten-free strawberry cream cheese filled muffins with crumble topping on a cooling rack.

Easy Gluten-Free Strawberry Muffins with Cream Cheese

Gluten-Free diet-friendly recipe
This is the best-tasting recipe for gorgeous Gluten-Free Strawberry Muffins with a cream cheese filling and a simple crumble on top. These healthy strawberry muffins are gluten-free with almond flour and cassava flour and include cottage cheese, unsweetened applesauce, eggs, cinnamon, cream cheese, toasted almonds, and lemon juice. You'll be proud to serve them for Mother's Day, brunches, showers, Easter, or any special occasion.
5 from 6 votes
Servings 12
Prep Time 25 minutes
Cook Time 25 minutes
Total Time 50 minutes

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

YouTube video

Notes

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.

Nutrition

Calories: 278kcalCarbohydrates: 24gProtein: 5gFat: 18gSaturated Fat: 5gPolyunsaturated Fat: 1gMonounsaturated Fat: 5gTrans Fat: 0.1gCholesterol: 64mgSodium: 156mgPotassium: 63mgFiber: 2gSugar: 11gVitamin A: 318IUVitamin C: 8mgCalcium: 109mgIron: 1mg
Keyword breakfast, cassava flour, cream cheese filling, crumble, strawberries
Did you make this recipe?Please let me know in the comments below how it turned out 🙂

5 Comments

  1. 5 stars
    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!

    1. Thank you so much for your review, Katie!!! I love that you love them as much as I do 🙂

  2. 5 stars
    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!

    1. You’re so welcome, Wendy! I’m so glad you love these muffins 🙂 Adding the chopped almonds to the crumble is a great idea!

  3. 5 stars
    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 🙂

5 from 6 votes (3 ratings without comment)

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