Apple Pie Cupcakes with Cinnamon Cream ‘Cheese’ Frosting

With the chillier weather, it’s time to pre-heat the oven so we can begin baking my new favorite dessert, Apple Pie Cupcakes! 

Your kitchen will smell of warm apples and cinnamon spice filling as we upgrade a basic vanilla cupcake into these gourmet desserts. In our house, my boys are absolutely raving about the cinnamon dairy-free cream cheese frosting. I don’t think there’s much doubt we’ll be creating another batch to close out Thanksgiving dinner.

In this recipe, the latest in my Kitchen Craft series for Allergic Living, I’ll walk you through four easy sections. We’ll start by preparing the apple pie filling, then the vanilla cupcakes, and onto the cinnamon cream cheese frosting and assembling the cupcakes. 

You can choose to bake your favorite vanilla cupcakes recipe or save some time by using an allergy-friendly vanilla cake mix. I tested this recipe using Sensitive Sweets Basic Cake and Cupcake mix that is free from the Top 9 allergens and gluten-free. It worked well, but this is not an endorsement and I welcome you to use your preferred allergy-friendly box mix.

Apple Pie Cupcake Versatility 

For dairy-free cream cheese and margarine, some people like to use Violife* products. If you’re using them for the ingredients below, their dairy-free cream cheese comes in a 7-ounce container. That’s fine to use if you adjust the recipe by using 7 tablespoons of margarine, not 8.

This recipe is also easily adaptable. So, if you’re not allergic to dairy, for example, you can easily substitute with regular cream cheese. You can use a mix that’s gluten-free or uses wheat flour, again depending on your diet needs. 

Short on time? With proper storage, the filling, cupcakes and frosting can be made a couple days in advance – making assembly the day of quick and easy to do. 

Best of all, these cupcakes will capture the sweet essence of fall with just one bite.  

Thank you for following my Kitchen Craft series. I hope my allergy-friendly baking projects, such as these Apple Pie Cupcakes, inspire you to create your own beautifully crafted desserts. Don’t forget to share your creations on Allergic Living’s Facebook or tag us on Instagram. Inclusion never tasted so sweet. (Photo by Ashley Smith)

Apple Pie Cupcakes with Dairy-Free Frosting

Makes: 18- 24 cupcakes
Free of: top allergens and gluten

Ingredients for Apple Pie Cupcakes

Apple Pie Filling 

  • 3 Honeycrisp apples (about 3 cups once prepped) 
  • 2 tbsp water
  • 1 tbsp lemon juice
  • 1 tsp cinnamon (divided)
  • ½ cup brown sugar
  • ¼ tsp salt
  • 1 tbsp cornstarch + 2 tbsp water

Vanilla Cupcakes

Cream ‘Cheese’ Frosting

  • 8 oz dairy-free, soy-free cream cheese (See Violife note in Intro)
  • 8 tbsp dairy-free, soy-free margarine 
  • 1 tsp pure vanilla extract
  • 4 cups confectioners’ sugar, sifted
  • 1/2 to 1 tbsp cinnamon


  • 2-quart saucepan 
  • Cutting board
  • Apple peeler
  • Chopping knife 
  • Stirring spoon or spatula
  • Small bowl 
  • 12-cavity cupcake pan 
  • Cupcake liners
  • 2 medium-to-large mixing bowls
  • Electric hand mixer or stand mixer with whisk attachment 
  • Piping bag with star tip
  • Piping tip, knife, or apple corer
  • Optional: medium ice cream scooper

Instructions for Apple Pie Cupcakes

Apple Pie Filling

  1. Wash, peel and dice 3 Honeycrisp apples.
  2. Place diced apples into a 2-quart saucepan and add water and lemon juice. Begin sprinkling (1/4 of the 1 teaspoon) cinnamon over the apples, while stirring over medium heat for 5-10 minutes. 
  3. Once the apples have begun to soften, turn heat to low, and continue to sprinkle the remaining ¾ tsp of cinnamon over the apples.
  4. Add the brown sugar and salt into the apple mixture. Stir.
  5. In a separate small bowl, mix the cornstarch with the water. Once combined, add to the apple mixture. Continue to stir until it’s brought to a boil. 
  6. Set filling aside to cool. 

Vanilla Cupcakes

  1. Line cupcake pan with liners. 
  2. Prepare your favorite allergy-friendly vanilla cake mix according to the package or recipe instructions. 
  3. Evenly fill cupcake liners with medium-sized scooper or spoon. Fill ½ full if using a recipe with gluten and ¾ full if using a gluten-free mix. Cupcakes are done when a toothpick inserted into the middle of one comes out clean. Set pan aside to allow cupcakes to cool completely. 

Cinnamon Cream Cheese Frosting

  1. Using an electric hand mixer, mix the vegan cream cheese and margarine on low for approximately 1 minute.
  2. Add vanilla and confectioners’ sugar. Add 1/2 tablespoon of cinnamon (and adjust if you want it stronger). Mix on medium for 2-3 minutes or until it resembles frosting consistency. 
  3. Place bowl of frosting in refrigerator for 2-5 minutes to chill. 
  4. Once slightly chilled, scoop icing into decorating bag. Tip: If you find it tricky to scoop frosting into the bag, place the decorating bag into a tall glass. Then fold the top of the bag over the edge of the glass to create a cuff.  Scoop your frosting in. 

Assembling Cupcakes

  1. Core the middle of your cupcake using one of three methods. If using a decorating bag tip: insert the large circle end of the tip no farther than halfway into the cupcake. Twist and pull up to remove the cupcake center. If using a knife: cut a small circle in the middle of the cupcake by inserting the knife at a 45-degree angle. (This method results in an upside-down cone shape but that’s OK.) If using an apple corer: position over the center of the cupcake. Insert until halfway and lift out the cake center. 
  2. Using a small spoon, fill the center of the cupcake with the apple pie filling. Don’t overfill. 
  3. To pipe the frosting, start at the outside next to the liner. Take one continuous circular motion around the apple pie filling. As shown in photo, add more filling to the center, if desired.  

Note: Any left-over apple pie filling can be sealed in a glass jar and kept in a refrigerator for a week. Left over cupcakes should be sealed in an airtight container. 

Ashley Smith is the support group leader of NNMG Food Allergic Families of Los Angeles ( and a member of FAACT’s Diversity, Equity & Inclusion Advisory Board.

is the support group leader of NNMG Food Allergic Families of Los Angeles ( and a member of FAACT's Diversity, Equity & Inclusion Advisory Board.