Apple Cupcakes – The Cookie Rookie®

These apple cupcakes are topped with cinnamon cream cheese frosting for a dessert that is super delicious. Make them for the holidays or any time of year, and the whole family will love them!

apple cupcakes topped with buttercream frosting

Cupcakes with Apple

If you’re looking for the perfect dessert to make this holiday season, this apple cupcakes recipe will do the trick!

Moist cupcakes with apple pieces in each bite are bound to win everyone over. Plus the cinnamon cream cheese frosting makes them even better. Make them for Thanksgiving if you want a single-serving dessert and fewer dishes (who doesn’t want that)!

Why You’ll Love this Apple Cupcake Recipe:

  • Easy-to-make: Cupcakes are notoriously easy to make, so cupcakes with apple are just as simple! Just follow this easy recipe step-by-step. You’ve got this!
  • Fall flavor: Apple is the flavor of fall so these cupcakes feel perfectly festive for the season!

Easy recipes like these cinnamon apple cupcakes are a great way to check off the dessert box this holiday season. If you’re feeling fancy, add a little caramel drizzle on top of your frosting for even more fun and decadence!

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

How to Make Apple Cupcakes

Be sure to see the recipe card below for full ingredients & instructions!

  1. Combine ingredients to make the batter, then fold in the apple slices.
  2. Fill the cupcake liners with batter, bake, and let them cool.
  3. Make the cinnamon cream cheese frosting, then frost cooled cupcakes.

Recipe Notes

  • Avoid using a dark pan when browning the butter. A white or light stainless pan will help you gauge the color of the butter.
  • Depending on the size of your muffin pan, you may end up with enough batter to make more than 12 cupcakes. You can bake them in a second muffin tin at the same time.
how to make apple cupcakes step by step photo instructions
apple cupcakes on a plate
What are apple cupcakes?

Apple cupcakes are delicious, warmly spiced cupcakes with fresh apple chunks folded in and topped with a rich, brown sugar cream cheese frosting. They’re a perfect fall treat!

What is the best type of apple for apple cupcakes?

Granny Smith apples are the best and most reliable to use in baking. They are naturally tart and sweet, which is perfect for baking!

Why aren’t my apple cupcakes rising properly?

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.

Why are my apple cupcakes dry?

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.

Do apple cupcakes need to be refrigerated?

Yes! Because these cupcakes are loaded with moist, fresh apple pieces and frosted with cream cheese, they will keep best in the refrigerator.

Why does my cream cheese frosting look curdled?

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.

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

Make Ahead Instructions

These apple cupcakes can be made up to 1 day in advance and stored in an airtight container in the refrigerator until ready to frost and serve.

The cream cheese frosting can be made up to 2 days in advance and stored in an airtight container in the refrigerator until ready to use. Let come to room temperature before using. You may need to rewhip the frosting for the best consistency.

Storage Instructions

Store leftover apple cupcakes in an airtight container in the refrigerator for up to 3 days. Enjoy cold or at room temperature.

Freezing Instructions

Freeze unfrosted apple cupcakes in a single layer on a lined baking sheet until solid, about 1-2 hours. Transfer to an airtight container or Ziplock bag to store for up to 3 months.

Freeze cream cheese frosting in a Ziplock bag for up to 1 month. Let thaw overnight in the refrigerator before using.


  • If using salted butter, omit the kosher salt.
  • For gluten-free apple cupcakes, swap the all-purpose flour for a gluten-free 1:1 baking flour.
  • For richer-flavored cupcakes, use dark brown sugar instead of light.
  • You can use any milk you like, including plant-based milk.
  • While I recommend Granny Smith apples, you can also use Gala, Honeycrisp, or Pink Lady.
  • In place of the heavy cream, you can use half-and-half.

Decorating Ideas

  • Top them with a sprinkle of cinnamon, a cinnamon stick, or an apple wedge!
  • Drizzle them with caramel sauce or apple cider sauce.
  • Add a turkey or leaf-shaped piece of pie crust for the Thanksgiving table!

Tips for the Best Apple Cupcakes

  • 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.
  • Be sure to use full-fat, brick-style cream cheese for the best frosting. Low-fat or spreadable cream cheese will not work!
apple cupcakes

I hope you love these fun and flavorful apple cupcakes as much as I do! If you’re looking for even more delicious desserts, check out the other holiday-themed recipes below!

If you make this recipe be sure to upload a photo in the comment section below or leave a rating. Enjoy!

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