Apple picking season is my favorite time of year, and it’s also the perfect time to bake up a batch of these apple cupcakes with cinnamon cream cheese frosting. These warmly spiced cupcakes are studded with fresh apple chunks, which makes them super moist and flavorful. The tangy cream cheese frosting perfectly balances their flavor, making this a great option for the holidays. I love to make these apple cupcakes as a delicious first-day-of-school treat for my kiddos.

apple cupcakes topped with buttercream frosting

This post may include affiliate links that earn us a small commission from your purchases at no extra cost to you.

These moist apple cupcakes topped with cream cheese frosting are not too sweet, which makes them one of my favorite Thanksgiving desserts, too. After eating all that heavy sweet and savory food, it’s nice to have a cupcake that’s not too cloyingly sweet to finish off the meal. They work great with just about any variety of apple, and they’re a great alternative to a more traditional apple pie.

What’s in This Apple Cupcake Recipe?

Butter: Unsalted butter makes the cupcakes rich, moist, and tender and forms the creamy base of the frosting. If using salted butter, I recommend omitting the kosher salt.
Flour: All-purpose flour gives these cupcakes structure.
Leavening: A combination of baking soda and baking powder helps these cupcakes rise to become light and fluffy.
Salt: Enhances the overall flavor of the cupcakes and the frosting.
Cinnamon: Adds warmth to the cupcakes and the frosting.
Sugar: A combination of brown and granulated sugar sweetens the cupcakes and deepens their flavor, while a combination of powdered sugar and brown sugar sweetens the frosting and deepens its flavor.
Eggs: Bind the cupcakes and help keep them moist.
Milk: Adds additional moisture to the cupcakes to create a cohesive batter. Any milk will work here, including plant-based options.
Vanilla Extract: Enhances the warm and sweet flavors in the cupcakes and the frosting.
Apple: Finely chopped apple adds texture and fresh apple flavor to the cupcakes. While I recommend Granny Smith apples, you can also use Gala, Honeycrisp, or Pink Lady.
Cream Cheese: Makes the frosting rich, creamy, and tangy. Be sure to use full-fat, brick-style cream cheese for the best frosting. Low-fat or spreadable cream cheese will not work!
Heavy Cream: Helps thin the frosting to the correct consistency for piping. Use half-and-half for a slightly lighter frosting.

overhead view of apple cupcakes arranged on a table top with apple slices

Tips for Success

Avoid using a dark pan when browning the butter. A white or light stainless pan will help you gauge the color of the butter.
Use room temperature ingredients for the best results (this includes the browned butter!)
Depending on the size of your cupcake tin, you may end up with enough batter to make more than 12 cupcakes. You can bake them in a second cupcake tin at the same time.
Don’t overfill the cupcake wells or your cupcakes may spill over.
If your cupcakes are a bit flat, that’s most likely because you didn’t add enough baking powder or baking soda. Also, be sure to check the expiration date on your baking powder/soda! If they’re expired, they just won’t do the trick.
Dry cupcakes can be caused by 2 things. You may have measured the ingredients incorrectly, or you might have overmixed the batter. It’s important to spoon and level your ingredients if you’re not using a scale, and it’s important to have a light hand when mixing the batter.
If your frosting looks curdled, it is likely too cold. Place the frosting in a heat-proof bowl set over a pot of simmering water until the edges begin to melt, then whip again until it comes together.

How to Store and Reheat

Store leftover apple cupcakes in an airtight container in the refrigerator for up to 3 days or in the freezer for up to 3 months. Let thaw overnight in the refrigerator before enjoying at room temperature.

side view of a cupcake with a bite taken out of it

Serving Suggestions

These apple cupcakes are such a great easy Thanksgiving dessert. I like to top them simply with a sprinkle of cinnamon, a cinnamon stick, or an apple wedge. They’re also super yummy drizzled with caramel sauce or apple cider sauce. To make them even more festive, try topping them with a turkey or leaf-shaped piece of pie crust.

How to Make Apple Cupcakes Step by Step

Brown the Butter: Preheat your oven to 350°F. Line a 12-count cupcake tin with paper liners and set aside. Add ½ cup of unsalted butter to a small saucepan set over medium heat. Once the butter has melted, begin stirring constantly until the butter gets foamy, then begins to brown. This will take 5-8 minutes. Once browned, pour the butter into a small bowl and set aside to cool.

Mix the Dry Ingredients: In a medium bowl, whisk 1½ cups of all-purpose flour, 1 teaspoon of baking soda, ¼ teaspoon of baking powder, ½ teaspoon of kosher salt, and 1 teaspoon of ground cinnamon together.

Whisk the Wet Ingredients: In a large bowl, whisk the browned and cooled butter, ½ cup of brown sugar, ½ cup of granulated sugar, 2 large eggs, ⅓ cup of milk, and 2 teaspoons of pure vanilla extract together.

Fold in the Apple: Add the dry ingredients to the wet and stir until just combined. Fold in 1 large peeled and finely chopped apple.

Bake the Cupcakes: Fill the cupcake liners ¾ of the way full (you may need more than 12). Bake for 20-25 minutes, or until a toothpick inserted into the center comes out with just a few moist crumbs. Let cool in the pan for 3 minutes, then transfer to a wire rack to cool completely.

apple mixture in cupcake liners, before baking

Beat the Butter: Using an electric mixer, beat 1 cup of unsalted butter until smooth, about 2 minutes.

Add the Cream cheese: Add in 8 ounces (1 brick) of cream cheese and beat until smooth, about 2 minutes.

Thicken the Frosting: Add in 1 teaspoon of vanilla extract and ⅛ teaspoon of salt, beating until incorporated. Turn the mixer down to low and slowly add in 4 cups of powdered sugar.

Flavor the Frosting: Add in ½ cup of brown sugar and 1½ teaspoons of ground cinnamon. Mix until well combined and creamy, another 1-2 minutes. Add in 3 tablespoons of the cream and mix until light and fluffy, about 3 minutes. If the frosting seems thick, add in the last tablespoon of cream and beat again.