Salted Caramel Apple Cupcakes {gluten-free}

Front-facing view of apple cupcakes on a plate, set atop a light pink linen. A tiny bowl of salt and apple slices are visible in the outer frame.
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5 from 6 reviews

If you’re a fan of caramel apples, you’ll love this festive fall cupcake recipe! Brown butter, brown sugar, and cinnamon add depth to these moist apple cupcakes, topped with a rich caramel buttercream frosting. For a little extra flair, finish them with a salted caramel drizzle and apple garnish.

  • Author: Alex Azary
  • Prep Time: 1 hour 5 minutes
  • Cook Time: 15-18 minutes
  • Total Time: 2 hours 23 minutes*
  • Yield: 15 cupcakes 1x
  • Category: cupcakes
  • Method: baking
  • Diet: Gluten Free



Salted Caramel Sauce

  • 1 cup (7 ounces) granulated sugar
  • 1 cup (8 1/4 ounces) heavy cream
  • ¼ teaspoon salt 

Apple Cupcakes:

  • 6 tablespoons (3 ounces) unsalted butter, cut into chunks
  • 1 ⅓ cups, spoon and level (5 5/8 ounces) + 2 tablespoons gluten-free all-purpose flour with xanthan gum, divided use
  • 1 ½ teaspoons baking powder
  • ¼ teaspoon salt
  • ¼  teaspoon baking soda
  • ⅛ teaspoon cinnamon
  • ½ cup (3 1/2 ounces) granulated sugar
  • ¼ cup, packed (1 7/8 ounces) brown sugar
  • 2 eggs, room temperature
  • ½ cup (4 1/4 ounces) buttermilk, room temperature
  • 1 teaspoon vanilla extract
  • 1 cup (4 1/2 ounces) peeled and minced Lucyglo apples

Salted Caramel Buttercream Frosting:

  • 12 tablespoons (6 ounces) unsalted butter, softened and cut into chunks
  • 6 ounces brick-style cream cheese
  • 6 tablespoons Salted Caramel Sauce 
  • 3 cups (12 ounces) powdered/confectioner's sugar
  • ¾ teaspoon vanilla extract
  • pinch of salt
  • Lucyglo apples, sliced (for garnish)
  • Flaky sea salt or fleur de sel (for garnish, optional)


Salted Caramel Sauce**:

  1. Add granulated sugar to a large, heavy-bottomed pot. Shake pot gently to spread sugar out in a thin, even layer across the bottom surface. Set on stove over medium-low heat and leave untouched as the sugar heats up and begins to melt. This step usually takes about 10 minutes, but the time can vary; watch it closely!
  2. Once the sugar is just beginning to melt, pour heavy cream into a microwave-safe container and microwave for about 1 minute, until very warm but not quite boiling.  Set aside nearby.
  3.  As the sugar melts, use a heat-safe spatula to gently push the melted sugar over the unmelted sugar; avoid excessive stirring. Continue to let cook until all of the sugar has liquified. Once this happens, begin to stir continuously, and cook just long enough for the melted sugar to reach a deep rust color. 
  4.  Once the sugar is melted and caramelized, slowly pour in the warm cream while stirring. Be extremely careful while doing this - the caramel will boil and produce very hot steam. (You may want to wear an oven mitt on the hand that will be stirring.) Continue to stir as the bubbling subsides, and cook for about 2 more minutes. At this point, the caramel should be noticeably thicker. 
  5. Remove caramel from heat and carefully pour into a mason jar (place a metal spoon in the jar to prevent it from shattering). Stir in salt. Set aside to cool to room temperature; it should thicken to a pipeable consistency once cool. 

Apple Cupcakes:

  1. Preheat oven to 350°F with racks in the top and bottom-third positions. Line two muffin pans with cupcake liners (this recipe makes enough for 15 cupcakes). 
  2. Place unsalted butter in a small skillet set over medium-low heat. Allow to cook, whisking occasionally, until the butter melts and begins to foam. Once foaming, whisk constantly until the butter turns golden-brown. Remove from heat and transfer to a large mixing bowl. Set aside to cool for at least 10 minutes. Meanwhile, prep the dry ingredients.
  3. In a second, medium mixing bowl, whisk together 1 ⅓ cups (5 5/8 ounces) flour with the baking powder, salt, baking soda, and cinnamon. Set aside.
  4. Add granulated sugar and brown sugar to the melted butter. Use a hand mixer to beat on medium speed for 30-60 seconds, until well-combined. Add the eggs one at a time, beating each in until incorporated. Continue beating for about another 30 seconds, until the mixture is slightly paler in color. 
  5. In a liquid measuring cup, combine buttermilk and vanilla extract.
  6. With the mixer on low speed, add ⅓ of the dry ingredients to the batter, followed by ½ of the buttermilk mixture. Continue alternating between the two, mixing as you go, and ending with the final portion of the dry ingredients. Mix just until the batter comes together evenly; do not overmix.
  7. In a small bowl, toss the apples with the remaining 2 tablespoons flour, to coat. Add to the batter and fold in by hand just until evenly dispersed.
  8. Divide batter evenly between the 15 cupcake liners, filling each about ⅔ full. Gently smooth out the surface of each cupcake. Transfer to preheated oven and cook for 15-18 minutes, switching and rotating the pans halfway through. The muffins should be nicely domed when done, and a toothpick inserted into the center of one should come out clean, or with just a few moist crumbs. 
  9. Allow muffins to cool in pans for about 10 minutes, and then transfer to a wire rack to cool completely before frosting. 

Salted Caramel Buttercream Frosting:

  1. In the bowl of a stand mixer fitted with the paddle attachment, combine the butter and cream cheese. Beat on low speed until smooth and well-combined. 
  2. Scrape down the bowl and beater and add 6 tablespoons of the cooled salted caramel sauce, along with the powdered sugar, vanilla extract, and salt. Switch to the whip attachment and beat on medium-low speed, just until all ingredients are evenly combined and the frosting is thick, fluffy, and smooth. 
  3. Spread or pipe frosting onto the cooled cupcakes. Transfer the remaining salted caramel sauce to a piping bag fitted with a small round tip, and drizzle caramel over frosted cupcakes. Garnish each cupcake with a small apple slice, and a sprinkle of salt, if desired. 
  4. Cupcakes are best served fresh, but keep well in the refrigerator for 3-5 days. Store leftovers in an airtight container. 


*Total time does not include any chilling time. 

**If you've never made caramel before, or are new to using the dry method, I highly recommend reading through this post on caramel sauce