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Apple Cheesecake Muffins with a creamy cheesecake center, cinnamon apples, and buttery crumb topping make an irresistible fall treat.
Know Before You Scroll
What You’ll Need
Flour, sugar, butter, cream cheese, eggs, milk, apples, orange juice, cinnamon, and a few basic baking staples.
Flavor Profile
Buttery vanilla muffin, tangy cheesecake, soft cinnamon apples, and a sweet cinnamon crumb topping.
Difficulty Level
Moderate. Nothing is technically difficult, but there are three simple components to prepare before assembling.
Equipment Needed
12-cup muffin pan, paper liners, mixing bowls, electric mixer, small saucepan, whisk or wooden spoon, and wire cooling rack.
Top Tip
Keep the apple mixture thick. It should hold together when spooned rather than have liquid pooling around the apples.
Time-Saving Tips
Make the apple filling first and let it cool while you prepare the muffin batter and cheesecake mixture.
Ingredient Swaps
Tart baking apples can be replaced with any firm apple that holds its shape when cooked. Lemon juice can replace the orange juice for a slightly sharper flavor.
Why This Recipe Works
These Apple Cheesecake Muffins look simple from the outside, but cut one open, and you get a creamy cheesecake layer with soft cinnamon apples tucked into the middle.
The cream cheese in the muffin batter does more than add flavor, it makes the batter thick enough to support that generous filling while keeping the crumb tender. I also cook the diced apples briefly and thicken their juices before assembling, so you get soft pieces of apple without adding excess moisture to the muffins.
And there’s no need to fuss over perfect layers. Spoon in the cheesecake and apples, cover with the remaining batter, and let the oven do the rest.
Ingredient Notes
Apples
Best Choice
Use a firm cooking apple with enough tartness to balance the sweet muffin and cheesecake filling. Granny Smith, Braeburn, or Pink Lady are all good choices.
Substitutions
Any firm apple that doesn’t turn to mush when briefly cooked will work.
Cream Cheese
Best Choice
Full-fat block cream cheese gives you the best texture. It’s used in both the muffin batter and cheesecake center, but for different reasons, the cream cheese in the batter adds flavor and gives it enough body to support the filling.
Substitutions
Neufchâtel can work, although the texture may be slightly softer. I wouldn’t use whipped cream cheese here.
Orange Juice
Best Choice
Fresh orange juice adds acidity and a subtle citrus flavor without making the apples taste overtly orange.
Substitutions
Lemon juice works well if that’s what you have. Because it’s more tart, you can use slightly less to taste.
Where to Find
Insert here
Cinnamon
Best Choice
Regular ground cinnamon works perfectly here and flavors both the apple filling and buttery crumb topping.
Substitutions
Apple pie spice can be used for a warmer, more spiced version.
Where to Find
Insert here
You can find the full, printable recipe at the top of this post, but you can read the detailed instructions with photos for each step below.
Step By Step Instructions
1
Prepare the Apples
Peel, core, and dice the apples into roughly ¼-inch pieces. Toss them with 1 tablespoon of orange juice, then coat evenly with the cornstarch.
2
Prepare the Apples
Melt the butter in a small saucepan and add the remaining orange juice, sugar, cinnamon, and salt. Add the apples and cook for 3 to 5 minutes, until they’re beginning to soften.
You’re not trying to cook them into applesauce. You should still be able to see the diced pieces, and the liquid around them should be thick enough to cling to the apples. Set aside to cool.
3
Make the Muffin Batter
Beat the butter, 2 ounces of cream cheese, sugar, and egg until pale and well blended. Mix in the milk.
Add the flour, baking powder, and salt and mix just until combined. The batter will be fairly thick, that’s intentional. It needs enough structure to hold the filling.
4
Make the Cheesecake Filling
Beat the 4 ounces of cream cheese with the sugar, egg yolk, and vanilla until smooth and creamy.
5
Fill The Muffins
Spoon enough muffin batter into the lined pan to fill each cup about one-quarter full.
Add a rounded tablespoon of cheesecake mixture followed by about a tablespoon of apple filling. Divide the remaining muffin batter over the top.
There’s no need to carefully spread or seal the batter around the filling. Just spoon it over and let it settle naturally as the muffins bake.
6
Add The Cinnamon Crumb & Bake
Combine the melted butter, sugar, flour, and cinnamon until the mixture forms moist crumbs. Divide it over the tops of the muffins.
Bake at 375°F/190°C for 20 to 25 minutes, until risen and golden.
Allow the muffins to cool in the pan for about 5 minutes before transferring them to a wire rack.
7
Cool & Serve
Allow them to cool completely before serving so the cheesecake and apple center has time to set. Serve at room temperature for the best flavor and texture.
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Recipe
Apple Cheesecake Muffins
Ingredients
For the Muffins
- 1¾ cups all-purpose/plain flour
- ¾ cup granulated sugar
- 2 teaspoons baking powder
- ¼ teaspoon salt
- 1 large egg
- ½ cup milk
- 2 ounces cream cheese (softened)
- 4 tablespoons butter (softened)
For the Cheesecake Filling
- 4 ounces cream cheese (softened)
- ¼ cup granulated sugar
- 1 egg yolk
- 1 teaspoon vanilla extract
For the Apple Filling
- 2 medium cooking apples
- 2 tablespoons orange juice (divided)
- 1 tablespoon butter
- 2 tablespoons granulated sugar
- 2 teaspoons cornstarch
- ¼ teaspoon ground cinnamon
- Pinch of salt
For the Cinnamon Crumb Topping
- ¼ cup butter (melted)
- ¼ cup granulated sugar
- ¼ cup all-purpose/plain flour
- ¼ teaspoon ground cinnamon
Instructions
- Preheat the oven to 375°F/190°C. Line a 12-cup muffin pan with paper liners.
- Peel, core, and dice the apples into approximately ¼-inch pieces. Toss with 1 tablespoon of the orange juice, then add the cornstarch and toss until evenly coated.
- Melt 1 tablespoon butter in a small saucepan over medium heat. Add the remaining tablespoon of orange juice, sugar, cinnamon, and salt. Add the apples and cook for 3 to 5 minutes, stirring regularly, until they begin to soften and the juices have thickened enough to cling to the fruit. If the mixture becomes too thick before the apples soften, add a small splash of orange juice. Remove from the heat and set aside to cool.
- To make the muffin batter, beat the softened butter, 2 ounces cream cheese, sugar, and egg until pale and well blended. Mix in the milk.
- Add the flour, baking powder, and salt and mix just until combined. Don’t overmix.
- To make the cheesecake filling, beat the 4 ounces cream cheese, sugar, egg yolk, and vanilla together until smooth.
- Divide enough muffin batter among the prepared cups to fill each approximately one-quarter full.
- Spoon a rounded tablespoon of cheesecake filling into the center of each, followed by approximately 1 tablespoon of the apple mixture.
- Divide the remaining muffin batter over the filling. There’s no need to spread it perfectly.
- Make the topping by combining the melted butter, sugar, flour, and cinnamon until moist crumbs form. Divide evenly over the muffins.
- Bake for 20 to 25 minutes, or until the muffins are risen and golden.
- Cool in the pan for 5 minutes, then transfer to a wire rack and allow to cool completely.
Tips
Erren’s Top Tips
Keep the apples small. A small dice means you get apple throughout the center without large pieces breaking up the muffin. Don’t overcook the apples. Three to five minutes is enough to give them a head start. They’ll continue cooking inside the muffins. Watch the consistency rather than the clock. The apple mixture should be thick with no loose juice pooling in the pan. If it becomes overly thick before the apples soften, add a small splash of orange juice. Don’t thin the muffin batter. It’s supposed to be thicker than an everyday muffin batter. That thickness helps keep the cheesecake and apple filling suspended in the center. Don’t overmix once the flour goes in. Mix only until you no longer see dry streaks of flour. Let them cool. The cheesecake center continues to set as the muffins cool, so resist cutting into one straight from the oven.Variations & Add-Ins
Apple Pie Spice: Replace the cinnamon in the apple mixture with apple pie spice for extra warmth. Add Nuts: Chopped pecans or walnuts can be added to the crumb topping for crunch. Caramel Apple: Drizzle completely cooled muffins with a little caramel sauce just before serving. Pear Cheesecake Muffins: Firm pears can replace the apples for a softer, more delicate fruit filling.Storage & Freezing
Because these muffins contain a cheesecake filling, I recommend storing them covered in the refrigerator once completely cooled. They’ll keep well for about 3 to 4 days. For the best texture, let a refrigerated muffin sit at room temperature for 15 to 20 minutes before eating. To freeze, cool the muffins completely and wrap them individually before placing them in an airtight freezer container or freezer bag. Freeze for up to 2 months. Thaw overnight in the refrigerator.
Save to favoritesYour saved recipes will be right here waiting for you every time you visit, so you can easily find and make the meals you love.FAQs
What are the best apples for apple muffins?
Firm apples that retain some texture when cooked are best. Granny Smith gives you plenty of tartness, while Braeburn and Pink Lady provide a sweeter balance. Very soft apples can break down too much during the initial cooking and subsequent baking.
Why is my muffin batter so thick?
It’s supposed to be. The cream cheese makes this batter thicker than a conventional muffin batter, which helps it support the relatively heavy cheesecake and apple filling.
Do Apple Cheesecake Muffins need to be refrigerated?
Yes. Because the muffins have a substantial cream cheese and egg-based cheesecake filling, I recommend refrigerating them once they’ve cooled.
Can I make the apple filling ahead?
Yes. Prepare the apple mixture, cool it completely, cover, and refrigerate it until you’re ready to bake. I would use it within a day or two.
Why did my cheesecake filling sink?
A very thin muffin batter, overly warm filling, or too much filling can make the center more likely to sink. With this recipe, don’t be tempted to thin the batter, it has deliberately been formulated to be thick enough to support the center.
Can I use apple pie filling instead?
I wouldn’t recommend standard canned apple pie filling without modification. It tends to contain considerably more sauce than we want here. This filling is deliberately thick because it’s being enclosed inside muffin batter.
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