Apple Streusel Muffins
These Apple Streusel Muffins are packed with fresh apples and a creamy cheesecake filling, then sprinkled with a cinnamon streusel topping. One of the best fall breakfast recipes!
You’ve got to try the Apple Coffee Cake with Streusel Toppings, Cinnamon Pancake Mix Muffins and Cheesecake Cornbread Muffins!

Once the weather cools down, I put my oven to work baking cozy seasonal treats like Apple Coffee Cake and Baked Apples.
Right now, I’m loving these apple cinnamon streusel muffins. With their rich apple-cinnamon flavor and surprise cream cheese filling, they taste like dessert for breakfast, and they’re incredibly easy to make.
This recipe is perfect for hosting, too. Bake a batch a day or two ahead and have them ready for overnight guests during the holidays. Trust me, these muffins are a fall favorite you’ll want on repeat.

Ingredients for Apple Streusel Muffins:
This apple cinnamon streusel muffins recipe has three components: the apple muffin batter, the cream cheese filling, and the cinnamon streusel topping. Don’t worry, many of the ingredients are used more than once!
- All-purpose flour
- Baking powder
- Ground cinnamon
- Salt
- Cream cheese
- Granulated sugar
- Light brown sugar
- Almond extract
- Unsalted butter
- Coconut oil
- Milk
- Eggs
- Apples

How to Make:
This is an incredibly easy apple muffin recipe, despite having a few extra steps. Here’s an overview of how the recipe comes together:
- In a large bowl, whisk together the flour, baking powder, cinnamon, and salt. Set aside.
- Make the cream cheese filling: In a medium bowl, beat 4 ounces of the softened cream cheese, ½ cup granulated sugar, and almond extract until smooth. Set aside.
- Make the streusel topping: In another bowl, combine the brown sugar, granulated sugar, cinnamon, melted butter, and flour. Stir well until it resembles wet sand. Set aside.
- Make the muffin batter: In another bowl, beat the remaining 4 ounces of cream cheese and remaining 1 ½ cups granulated sugar until fluffy.
- Add oil and milk, beating until smooth. Add eggs, beating until combined.
- Stir in shredded apples and flour mixture until well combined.
- Spoon the batter into 14 lined muffin cups. Drop cream cheese mixture into center of the batter. Then, sprinkle brown sugar streusel over batter

How to Store Cream Cheese Apple Muffins:
Because the cream cheese is baked into the muffins, it’s safe to store these at room temperature. They’ll last up to three days in an airtight container.
Can These Muffins Be Frozen?
Yes! Let them cool completely on your countertop, then seal inside a freezer bag. When ready to eat, thaw on the counter for a couple hours.
Can the Cream Cheese Filling Be Omitted?
If you’d like to make classic apple streusel muffins, you should be fine to omit the cream cheese filling.
However, you’ll still need to add cream cheese directly to the muffin batter, as instructed. The cream cheese in the muffin batter makes the finished muffins incredibly rich and moist.

Tips and Tricks:
- I prefer making this recipe with either Honey Crisp or Granny Smith apples. Both are fairly hearty and shred well.
- You can shred the apples using the side of a box grater, or in a food processor (if it came with a shredding blade).
- Make sure to use brick-style cream cheese in this recipe rather than the whipped kind that comes in a tub.
Looking for More Fall Muffin Recipes? I’ve Got You Covered!
- Apple Cinnamon Muffins
- Pumpkin Apple Muffins
- Pumpkin Blueberry Muffins
- Pumpkin Nutella Muffins
- Peanut Butter Chocolate Chip Muffins

Cream Cheese Apple Streusel Muffins
Ingredients
- 3 cups all-purpose flour
- 1 tablespoon baking powder
- 1 teaspoon ground cinnamon
- 1 teaspoon salt
- 1 package (8 ounce) cream cheese, softened and divided
- 2 cups granulated sugar, divided
- ¼ teaspoon almond extract
- 2 tablespoons unsalted butter, softened
- ½ cup melted coconut oil, (or vegetable oil)
- ⅓ cup milk, any kind, (I used 2%)
- 2 eggs
- 1½ cup shredded peeled Honey Crisp or Granny Smith apple, About 2 medium apples
Cinnamon Streusel Topping
- ¼ cup packed light brown sugar
- ½ tablespoons granulated sugar
- 1 teaspoon ground cinnamon
- 2 tablespoons unsalted butter, melted
- ⅓ cup all-purpose flour
Instructions
- Preheat oven to 350°F. Line 2 muffin tins with paper liners (about 14-15 muffin cups). Set aside.
- In a large bowl, whisk together flour, baking powder, cinnamon, and salt. Set aside.
- In a medium bowl, beat 4 ounces softened cream cheese, ½ cup granulated sugar, and almond extract with an electric hand mixer or stand mixer with fitted paddle attachment at medium speed until smooth. Set aside.
- To make the streusel topping, in another medium bowl, combine the brown sugar, granulated sugar, cinnamon, melted butter, and flour. Stir well until it resembles wet sand. Set aside.
- In another large bowl, beat remaining 4 ounces cream cheese and remaining 1½ cup granulated sugar until fluffy. Add oil and milk, beating until smooth. Add eggs, beating until combined. Stir in shredded apples and flour mixture until well combined.
- Spoon batter into prepared muffin cups, filling a little over ¾ full. Drop cream cheese mixture into center of batter. Then sprinkle brown sugar streusel over batter.
- Bake for 28-32 minutes, or until golden brown. Let cool in pan for 10 minutes. Then remove from pans and cool completely on a wire rack.
Notes
- Muffins will keep in an airtight container at room temperature for up to three days.
- Muffin recipe from Paula Deen’s Fall Baking Magazine – 2014