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Paleo Apple Pie Cupcakes

These Paleo Apple Pie Cupcakes are on a whole new level of heavenly! Moist and fluffy cupcakes are laced with warm fall spices, stuffed with homemade apple pie filling, topped with honey butter frosting, then finished off with a drizzle of caramel sauce.

Three paleo cupcakes on a piece of parchment paper with a pan containing more cupcakes behind them

Fluffy Gluten-Free Cupcakes With Apple Pie Filling

Whenever you make these cupcakes for a special event, people will be asking where you bought them. They have that fancy bakery feel, and no one will be able to tell that they’re gluten-free and paleo. They may not look a thing like apple pie, but all of those crowd-favorite flavors come through in every single bite.

What really makes these cupcakes special is that each part is uniquely delicious on its own – and they all complement one another so well. The cupcakes are perfectly spiced, the filling provides a pop of caramelized apple goodness, the frosting is smooth as velvet, and the caramel sauce adds a decadent finishing touch. What more could you possibly wish for?

Apples, cinnamon, nutmeg, a lemon and the rest of the filling ingredients on a countertop

What You’ll Need

Most cupcakes with a filling, a frosting and a caramel drizzle are glorified sugar bombs, but these ones have an unusually wholesome ingredient lineup. The amounts you’ll need are included in the recipe card below this post.

Spiced Cupcakes

  • Almond Flour: Flour should always be fluffed up and spooned into the measuring cup little by little to prevent overpacking – no matter what kind you’re working with
  • Tapioca Flour
  • Coconut Flour: These different types of flour come together to keep your cupcakes nice and fluffy.
  • Baking Powder
  • Sea Salt
  • Ground Cinnamon
  • Nutmeg
  • Ground Ginger
  • Ground Cloves
  • Unsalted Grass-Fed Butter: Melted and cooled.
  • Pure Maple Syrup: Make sure you stay away from the artificial stuff.
  • Large Eggs: Brought to room temperature and whisked.
  • Pure Vanilla Extract
  • Coconut Cream: You can buy this as-is or skim it off the top of a chilled can of coconut milk.

Apple Pie Filling

  • Medium-Sized Apples: Peeled, cored and diced.
  • Unsalted Grass-Fed Butter
  • Coconut Sugar
  • Lemon Juice: Freshly squeezed from 1/4 of a lemon.
  • Cinnamon
  • Sea Salt
  • Nutmeg
  • Ground Ginger
  • Ground Cloves

Maple Butter Frosting

  • Unsalted Grass-Fed Butter: Room temperature.
  • Raw Honey
  • Vanilla
  • Tapioca Flour: Or arrowroot flour.
  • Coconut Flour
  • Sea Salt

Paleo Caramel Sauce

  • Water
  • Raw Coconut Sugar
  • Coconut Milk: Or your preferred alternative.
  • Vanilla Extract
  • Pinch of Salt

A spiced cupcake topped with honey butter frosting with more cupcakes in the background

How to Make Paleo Apple Pie Cupcakes

Take this recipe one step at a time and you’ll be done before you know it. Each component comes together with ease, and you can whip up the filling, the frosting and the caramel while the cupcakes bake and cool.

Make the Cupcakes

  1. Prep for Baking: Preheat the oven to 350°F and line a 12-cup cupcake pan with nonstick liners. Set the prepared pan aside.
  2. Combine Dry Ingredients: Stir together the flours, baking powder, salt and spices in a medium-sized bowl until thoroughly combined. Set the mixture aside.
  3. Combine Wet Ingredients: Whisk together the butter, maple syrup, eggs, vanilla and coconut cream in a large bowl until smooth.
  4. Add Dry Ingredients: Add the flour mixture to the butter mixture and stir until combined (add half or 1/3 at a time if needed).
  5. Bake: Divide the batter evenly between your liners and bake the cupcakes for 18 minutes, or until a toothpick inserted into the center comes out clean.
  6. Let Cool: Remove the cupcakes from the oven and allow them to cool completely.
  7. Remove Centers: Use a knife to carefully cut a square into the center of each cooled cupcake. Scoop out the center of the cupcake, making a small well for the apple pie filling.

A collage of two images with one showing the squares being cut out of the cupcakes and the other showing the cored cupcakes

Make the Filling

  1. Melt Butter: Melt the butter in a nonstick skillet over medium-high heat.
  2. Cook Apples: Add in the diced apples and cook them for about 5 minutes, stirring occasionally, until they’ve softened up a bit.
  3. Add Sugar & Spices: Stir in the coconut sugar, salt, cinnamon, nutmeg, ginger and ground cloves.
  4. Continue Cooking: Cook the filling for 5 more minutes, or until the apples are tender.
  5. Add Lemon Juice: Squeeze in the lemon juice and stir to combine. Set the filling aside to cool.
  6. Spoon Into Cupcakes: Spoon the completely cooled filling into the wells you made in each cooled cupcake.

Homemade apple pie filling inside of a skillet on a kitchen countertop

Prepare the Caramel

  1. Boil Water & Sugar: Bring the water and coconut sugar to a boil, stirring the mixture constantly.
  2. Add Coconut Milk, Vanilla & Salt: Stir in the coconut milk, vanilla extract and salt.
  3. Cook: Let the caramel cook over medium heat for 10-15 minutes, stirring constantly so that it doesn’t burn. The mixture will start to thicken and darken in color. Once you’ve seen this change happen, set it aside and let it cool.

Make the Frosting

  1. Add Ingredients to Bowl: Combine all of the frosting ingredients in a large mixing bowl.
  2. Whip: Blend it all together with an electric mixer on medium speed until the frosting is whipped.
  3. Pipe Onto Cupcakes: Transfer the frosting to a piping bag fitted with an open star tip and pipe a swirl of frosting onto each cupcake.
  4. Add Caramel: Drizzle some caramel sauce over each frosted cupcake, adding as much or as little as you’d like.

An unwrapped apple pie cupcake on a piece of parchment paper with the remaining cupcakes from the batch behind it

Can I Make Them in Advance?

You can get the filling, the caramel and the frosting done a day or two ahead of time if you want to break up the process. Refrigerate each component in its own airtight container, waiting until the filling and caramel have cooled before you store them. Bring the frosting and caramel to room temperature before you build the cupcakes (note that you might have to microwave the caramel for 10-15 seconds before you’re able to drizzle it).

If you’d rather make the cupcakes themselves in advance, store them in an airtight container at room temperature once they’ve cooled completely.

Tips for Success

One tip stands out above the rest – gobble up those cupcake centers you removed for the apple pie filling! You may not need them for the finished product, but they’re too yummy to go to waste.

  • Pick Firm Apples: I recommend using apples of a firmer variety like Honeycrisp, Fuji, Granny Smith or Pink Lady. Bonus points if it’s apple season and you picked them yourself. Avoid softer kinds of apples, which tend to get mushy when they’re cooked.
  • Remove the Skin: I know the apple skin has added health benefits, but it really doesn’t belong inside these cupcakes. It will toughen and separate from the apples while they cook, leaving you with unpleasant clumps in your filling.
  • Use a Cupcake Corer: If you happen to have a cupcake corer, go ahead and use it to make the wells for your filling. I personally prefer to cut out a square because I feel like it makes more room for the filling, but your corer will definitely get the job done more quickly.
  • Stir the Caramel Constantly: Caramel sauce burns super quickly, so you have to make sure it’s continuously moving around in the pan. Stir it constantly and you’ll have nothing to worry about.

A close-up shot of a pan of paleo apple pie cupcakes topped with frosting and caramel sauce

How to Store Extra Cupcakes

Keep any leftover cupcakes refrigerated in an airtight container. Enjoy them within 3 days for the best results.

Can I Freeze These?

These cupcakes are easier to freeze than you might imagine – frosting, caramel and all. Spread out the finished cupcakes on a parchment-lined baking sheet and freeze them for 2-3 hours, or until they’ve solidified. Wrap each frozen cupcake in clear wrap or foil and freeze them in an airtight container for up to 2 months.

Unwrap your cupcakes and allow them to thaw in the fridge overnight before you enjoy them.

More Mouthwatering Apple Dessert Ideas

Paleo Apple Pie Cupcakes

These Paleo Apple Pie Cupcakes are on a whole new level of heavenly! Moist and fluffy cupcakes are laced with warm fall spices, stuffed with homemade apple pie filling, topped with honey butter frosting, then finished off with a drizzle of caramel sauce.
Prep Time15 mins
Cook Time45 mins
Total Time1 hr
Servings: 12

Equipment

  • Oven

Ingredients

For the Spiced Cupcakes

  • 3/4 cup almond flour
  • 1/3 cup + 3 tablespoons tapioca flour
  • 1/4 cup coconut flour
  • 11/2 teaspoons baking powder
  • 1/4 teaspoon sea salt
  • teaspoon ground cinnamon
  • 1/8 teaspoon nutmeg
  • 1/8 teaspoon ground ginger
  • 1/8 teaspoon ground cloves
  • 1/2 cup 1 stick grass fed unsalted butter, melted and cooled
  • 3/4 cup pure maple syrup
  • 2 large eggs whisked at room temperature
  • 1 teaspoons pure vanilla extract
  • 1/2 cup coconut cream

For the Apple Pie Filling

  • 2 medium sized apples peeled, cored and diced
  • 2 Tbsp unsalted butter
  • ¼ cup coconut sugar
  • lemon juice from a quarter lemon
  • ½ Tbsp cinnamon
  • 1/8 teaspoon sea salt
  • 1/8 teaspoon ground nutmeg
  • 1/8 teaspoon ground ginger
  • 1/8 teaspoon ground cloves

For the Honey Butter Frosting

  • 1 cup unsalted butter room temperature
  • 1/2 cup raw honey
  • 2 Tsp vanilla
  • 4 Tbsp tapioca flour or arrowroot flour
  • 4 Tbsp coconut flour
  • 1/4 tsp sea salt

For the Paleo Caramel Sauce

  • 2 tablespoons water
  • 1/4 cup raw coconut sugar
  • 1/2 cup coconut milk
  • 1 teaspoon vanilla extract
  • pinch salt

Instructions

Make the Cupcakes

  • Preheat the oven to 350° F degrees. Line a 12-cup cupcake/muffin pan with cupcake liners. Set aside.
  • In a medium sized bowl, stir together the flours, baking powder, salt and spices until thoroughly combined. Set aside.
  • In a large bowl whisk butter, maple syrup, eggs, vanilla and coconut cream together until smooth.
  • Add the flour mix into the butter mix and stir until combined.
  • Divide the batter between 12 liners in your cupcake pan. Bake for 18 minutes, or until a toothpick inserted in the center comes out clean.
  • Allow to cool completely, then use a knife to cut a square into the center of each cupcake. Scoop out that center square, making a small well for the apple pie filling.

Make the Filling

  • In a nonstick skillet, melt 2 tablespoons butter over medium-high heat.
  • Add apples; cook about 5 minutes, stirring occasionally, until softened. Sprinkle with 2 tablespoons coconut sugar, salt, cinnamon, nutmeg, ginger, and ground cloves.
  • Cook for 5 minutes or until apples is tender.
  • Squeeze in lemon juice and stir to combine.
  • Allow to cool completely, then spoon into cupcake wells.

Make the Caramel

  • Bring the water and coconut palm sugar to a boil stirring the mixture constantly
  • Add the coconut milk vanilla extract and salt and cook for 10-15 minutes over medium heat, stirring constantly so that it doesn't burn. The mixture will start to thicken and turn darker in color.
  • Set aside

Make the Frosting

  • In a mixing bowl, combine everything
  • Blend with an electric mixer or hand mixer on medium until whipped together
  • Put into a piping bag and top cupcakes.
  • Pipe frosting onto each cupcake.
  • Then drizzle paleo sauce over frosting. As much or as little as you like.
  • Store any unused paleo caramel sauce covered in the refrigerator.

Notes

  • To Store: Refrigerate extra cupcakes in an airtight container and enjoy within 3 days.
  • To Freeze: Spread cupcakes out on a parchment-lined baking sheet and freeze for 2-3 hours, or until solidified. Wrap each frozen cupcake in clear wrap or foil and freeze in an airtight container for up to 2 months. Unwrap and thaw in the fridge before enjoying.
Course: Dessert
Cuisine: American

Categories:

A collage of two images of apple pie cupcakes with a label introducing the dessert in between the photos

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4 comments on “Paleo Apple Pie Cupcakes”

  1. Avatar photo
    Shashi at RunninSrilankan

    Such a fantastic recipe! I so love the sound of these and woa – such a brilliant idea to add that apple pie filling into these cupcakes! So much texture and flavor in each bite!

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