Apple Cinnamon Muffins with Cream Cheese Filling
These apple cinnamon muffins are soft and full of cozy fall flavor. They’re filled with a smooth cream cheese center and finished with a crunchy streusel topping. The recipe makes 15 muffins and comes together quite easily if you follow the steps.
After pumpkin, apple is probably the second flavor that comes to mind when we think about fall. Apple pies, apple crisps, apple cookies… there are so many cozy recipes that make this season feel special. I recently made apple oatmeal cookies and they were such a hit that I knew I had to try another apple dessert right away. That’s how these apple muffins came to life and they turned out just as delicious and amazing. This recipe makes 15 muffins, which is the perfect amount for sharing or enjoying over a few days. They’re soft, full of cinnamon & apple flavor and filled with a smooth cream cheese center.
I already have so many apple muffin variations in my head and on my to do list. One of the ideas I can’t wait to try is a simple apple oatmeal cheesecake muffin. Sounds good right? If I don’t get to bake it this fall, it’s definitely coming next fall. For now though, these muffins are the perfect way to enjoy apple season. They’re beginner friendly and come together quickly.
WHY YOU’LL LOVE THIS RECIPE
♥ It’s the ultimate fall flavor combo - Pumpkin usually gets all the attention in fall, but apple deserves just as much love. These muffins combine apple, cinnamon and cream cheese for a cozy mix of flavors.
♥ The streusel topping adds crunch - Without the topping they’d still be tasty, but the streusel makes them super delicious.
♥ Beginner friendly and simple to make - You don’t need fancy equipment or special skills for this recipe. The steps are straightforward and I added notes and tips to help along the way.
♥ Small batch recipe - This recipe makes 15 muffins, which is not too much but not too little either.
Notes, tips and tricks
Let the muffins cool completely before filling: If you try to fill them while they’re still warm, the cream cheese filling will melt, so make sure to let them completely cool before moving on.
Let them come to room temperature before serving: When stored in the fridge, the muffins get a bit firm. Letting them sit for 20-30 minutes softens them up again, giving a better texture. If you forget, a quick 20 second pop in the microwave works like magic.
Try not to overbake them: Overbaking dries the muffins out and can make the edges too firm.
Frequently asked questions
1. How should I store these muffins?
Store the muffins in an airtight container in the fridge for up to 4 days. This keeps the cream cheese filling fresh.
2. Can I freeze these muffins?
Yes, you can freeze them wrapped tightly in plastic wrap and placed in a freezer bag. Thaw them at room temperature.
3. Why did my muffins turn out dry?
Dry muffins usually mean they were overbaked. Make sure to check the baking time carefully!
4. What kind of apples work best?
I used Pink Lady apples because they have a nice balance of sweetness and tartness.
5. Can I leave out the streusel topping or the cream cheese filling?
Yes! Both are optional. Without the streusel, you’ll have a simpler, classic apple muffin. Skipping the cream cheese filling makes them easier to store and a bit less rich, but the flavor is still delicious.
Ingredients you will need for this recipe
Caramelized apples:
Apples: I used Pink Lady Apples
Unsalted butter: Helps caramelize the apples.
Light brown sugar: Can substitute with dark brown sugar for a deeper flavor.
Cinnamon and Nutmeg: Classic fall spices that pairs beautifully with apples.
Vanilla extract: Vanilla bean paste works well for a more intense flavor.
Streusel:
Unsalted butter: Binds the flour and sugar into crumbly topping.
All purpose flour: Forms the structure of the streusel.
Sugar: Sweetens and caramelizes slightly during baking.
Muffins:
Unsalted butter: Adds richness and helps keep the muffins tender.
Granulated sugar: Sweetens the batter.
Light brown sugar: Dark brown sugar works as a substitute.
Eggs: Provide structure.
Vanilla bean paste or extract: Enhances the flavor.
Milk: Adds moisture and thins the batter slightly. You can substitute with plant based milk
Plain yogurt or sour cream: Adds moisture and a slight tang. Greek yogurt works too.
Al purpose flour: Main structure of the muffins.
Baking powder: Leavening agent that helps the muffins rise. Make sure it’s fresh for best results.
Cinnamon: Can mix with nutmeg or allspice for variation.
Filling:
Unsalted butter: Adds richness to the cream cheese filling.
Cream cheese: Main component of the filling.
Caster sugar: Sweetens the filling. Granulated sugar can work but may be slightly grainy.
Vanilla bean paste: Vanilla extract works as a substitute.
Step by step instructions with photos
1. First cook the apples.
2. In a saucepan melt the butter. Add the chopped up apples, brown sugar, cinnamon, nutmeg and vanilla. Cook over medium heat covered for 5 minutes, then take the cover off and cook for additional 15-18 minutes, stirring occasionally until they soften and the water evaporates. Once ready set aside.
3. Next, prepare the streusel.
4. In a bowl whisk together the flour, sugar and cinnamon; then add the melted butter and mix until it turns crumbly. Once ready, place in the fridge.
5. Preheat your oven to 180•C.
6. In a large bowl mix together the butter with the brown sugar and granulated sugar.
7. Next mix in the eggs and the vanilla bean paste.
8. Add the flour, baking powder, cinnamon, yogurt and milk; mix until combined.
9. Scoop into your muffin tin lined with cupcake liners.
10. Top each muffin with about a tablespoon of cooked apples, then sprinkle some streusel over them.
11. Bake in the preheated oven for 18 minutes.
12. For the cream cheese filling, mix together the softened butter with the sugar, then add the cream cheese along with the vanilla and mix until smooth. Transfer to a piping bag.
13. Once the cupcakes are done, make sure to let them completely cool before filling.

Apple Cinnamon Muffins with Cream Cheese Filling
These apple cinnamon muffins are soft and full of cozy fall flavor. They’re filled with a smooth cream cheese center and finished with a crunchy streusel topping. The recipe makes 15 muffins and comes together quite easily if you follow the steps.
Ingredients
- 3 apples, peeled and cut into small cubes
- 30g unsalted butter - 2 tablespoons
- 50g light brown sugar - 1/4 cup
- 2 teaspoons of cinnamon
- 1/4 teaspoon nutmeg
- 1 teaspoon vanilla extract
- 40g unsalted butter, melted - 3 tablespoons
- 70g all purpose flour - 1/2 cup + 1 tablespoon
- 35g sugar - 3 tablespoons
- 135g unsalted butter, softened - 1/2 cup + 1 tablespoon
- 100g granulated sugar - 1/2 cup
- 100g light brown sugar - 1/3 cup + 2 tablespoons
- 2 eggs
- 1 tsp vanilla bean paste or vanilla extract
- 100g milk - 1/3 cup + 1 tablespoon
- 180g plain yogurt or sour cream - 3/4 cup
- 220g all purpose flour - 1 cup + 2/3 cup
- 8g baking powder - 2 teaspoons
- 1 teaspoon cinnamon
- 50g softened butter, unsalted - 3 tablespoons
- 175g cream cheese - 3/4 cup
- 80g caster sugar - 1/3 cup + 1 tablespoon
- 1 teaspoon vanilla bean paste
Instructions
- First cook the apples.
- In a saucepan melt the butter.
- Add the chopped up apples, brown sugar, cinnamon, nutmeg and vanilla.
- Cook over medium heat covered for 5 minutes, then take the cover off and cook for additional 15-18 minutes, stirring occasionally until they soften and the water evaporates.
- Once ready set aside.
- Next, prepare the streusel.
- In a bowl whisk together the flour, sugar and cinnamon; then add the melted butter and mix until it turns crumbly.
- Once ready, place in the fridge.
- Preheat your oven to 180•C.
- In a large bowl mix together the butter with the brown sugar and granulated sugar.
- Next mix in the eggs and the vanilla bean paste.
- Add the flour, baking powder, cinnamon, yogurt and milk; mix until combined.
- Scoop into your muffin tin lined with cupcake liners.
- Top each muffin with about a tablespoon of cooked apples, then sprinkle some streusel over them.
- Bake in the preheated oven for 18 minutes.
- For the cream cheese filling, mix together the softened butter with the sugar, then add the cream cheese along with the vanilla and mix until smooth.
- Transfer to a piping bag.
- Once the cupcakes are done, make sure to let them completely cool before filling.
Nutrition Facts
Calories
321Fat
22 gSat. Fat
12 gCarbs
44 gFiber
19 gNet Carbs
44 gSugar
27 gProtein
12 gSodium
117 mgCholesterol
58 mg