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.

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?

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

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.

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.

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.

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.

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

• Apple Blondies
• Raspberry Apple Almond Cake
• Apple Nachos
• Apple Pecan Cake

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