Ultimate Chocolate Pecan Pie Cupcakes

Here is my favorite chocolate pecan pie cupcake recipe, with a rich chocolate cupcake base, a gooey pecan pie filling, and a simple whipped cream topping that brings it all together.

These cupcakes are what I make when I can’t decide between chocolate cake and pecan pie for dessert. They’re always gone within hours at potlucks, and my kids love helping me arrange the pecans on top. Plus, they’re way easier to serve than a whole pie!

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What Kind of Pecans Should I Use?

Raw pecans are what you’ll need for this recipe, and you can find them in the baking aisle or bulk section of most grocery stores. Fresh pecans should smell sweet and nutty, not bitter or rancid, so give them a quick sniff test before buying if possible. If you only have roasted pecans on hand, they’ll still work in a pinch, but raw pecans give you more control over the final flavor since they’ll toast up nicely as the cupcakes bake. Store any leftover pecans in the freezer to keep them fresh longer, as the oils in pecans can go bad pretty quickly at room temperature.

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Options for Substitutions

These cupcakes are pretty forgiving when it comes to swapping ingredients:

• Pecans: Walnuts make a great substitute if you don’t have pecans around. You could also try a mix of nuts like almonds and pecans for something different.
• Bourbon: Not a fan of bourbon or keeping it alcohol-free? Replace it with the same amount of vanilla extract mixed with water, or use apple juice for a subtle sweetness.
• Greek yogurt: Sour cream works perfectly in place of Greek yogurt at a 1:1 ratio. You can also use regular plain yogurt, though the batter might be slightly thinner.
• Coconut oil: Vegetable oil or melted butter are easy swaps here. Use the same amount and your cupcakes will turn out just fine.
• Maple syrup: Honey or corn syrup can step in for maple syrup, though you’ll lose that distinct maple flavor. Use the same measurement for either substitute.
• Coffee: The coffee deepens the chocolate flavor, but if you’re not a coffee person, just use hot water instead. You won’t taste the coffee in the final cupcake.
• Heavy cream: Whole milk or half-and-half can replace heavy cream in the frosting, though it might be slightly less rich. Add it gradually to get the right consistency.

Watch Out for These Mistakes While Baking

The biggest mistake when making these cupcakes is overmixing the batter once you add the flour, which can lead to dense, tough cupcakes instead of light and fluffy ones – mix just until the dry ingredients are incorporated and no streaks remain.

Since these cupcakes contain both coffee and bourbon, overbaking them will intensify those flavors and dry them out, so start checking for doneness at 16 minutes by inserting a toothpick in the center (it should come out with just a few moist crumbs).

When making the pecan topping, watch your brown sugar mixture carefully on the stovetop because it can go from perfect to burnt in seconds, and make sure your butter is truly at room temperature before making the frosting – cold butter will create lumps that are nearly impossible to smooth out.

Finally, let the cupcakes cool completely before frosting, otherwise the buttercream will melt and slide right off.

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What to Serve With Chocolate Pecan Pie Cupcakes?

These cupcakes are pretty rich and decadent on their own, so they’re perfect as a standalone dessert with a hot cup of coffee or a cold glass of milk. If you’re serving them at a party or gathering, consider setting out some vanilla ice cream on the side – the cold creaminess is a nice contrast to the warm bourbon and chocolate flavors. A simple whipped cream topping also works great if you want to add a lighter touch, or you could drizzle some extra maple syrup or caramel sauce over the top for anyone with a serious sweet tooth. These also pair nicely with after-dinner drinks like coffee, espresso, or even a small glass of bourbon to echo the flavors in the cupcakes.

Storage Instructions

Store: These cupcakes keep really well in an airtight container at room temperature for up to 3 days. If your kitchen is warm or you want them to last longer, store them in the fridge for up to 5 days. Just bring them to room temperature before serving so the frosting gets nice and creamy again.

Freeze: You can freeze these cupcakes for up to 3 months, either frosted or unfrosted. I like to freeze them individually wrapped in plastic wrap, then place them all in a freezer bag. If you’re freezing unfrosted cupcakes, you can make the frosting fresh when you’re ready to serve.

Thaw: Let frozen cupcakes thaw in the fridge overnight or on the counter for a couple hours. They taste just as good as fresh, and the pecan topping stays nice and crunchy even after freezing.

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 6900-7600
• Protein: 65-80 g
• Fat: 470-530 g
• Carbohydrates: 700-780 g

Ingredients

For the toasted pecans:

• 3 cups raw pecans
• 1/2 tsp ground cinnamon
• 2 tbsp packed brown sugar
• 2 tbsp bourbon
• 1 tsp vanilla extract

For the pecan pie filling:

• 1/4 cup cornstarch
• 4 large egg yolks (room temperature)
• 2 tsp vanilla extract
• 1/2 cup packed brown sugar
• 3/4 cup real maple syrup (for best flavor)

For the cupcakes:

• 3/4 cup unsweetened cocoa powder
• 1/2 cup strong black coffee
• 2 cups all-purpose flour (I use King Arthur flour)
• 3/4 tsp kosher salt
• 1 cup melted coconut oil (cooled slightly)
• 1/2 cup bourbon
• 1 cup granulated sugar
• 1 1/2 tsp baking soda
• 2 large eggs
• 2/3 cup plain Greek yogurt

For the frosting:

• 1 tbsp vanilla extract
• 12 tbsp salted butter (I prefer Kerrygold for richness)
• 4 tbsp salted butter
• 1/2 cup heavy cream
• 3 cups powdered sugar (sifted)
• 1 cup packed brown sugar

For the topping:

• 22 whole pecans

Step 1: Prepare and Toast the Pecans

• 3 cups raw pecans
• 2 tablespoons bourbon
• 1 teaspoon vanilla extract
• 2 tablespoons packed brown sugar
• 1/2 teaspoon ground cinnamon

Preheat your oven to 350°F and line a baking sheet with parchment paper.

On the sheet, combine the raw pecans, 2 tablespoons bourbon, 1 teaspoon vanilla extract, 2 tablespoons packed brown sugar, and 1/2 teaspoon ground cinnamon.

Toss well and bake for 8-10 minutes until the pecans are toasted and aromatic.

Once done, sprinkle with sea salt if you wish.

Roughly chop the pecans, saving 22 whole pecans for garnishing later.

Step 2: Cook and Chill the Pecan Pie Filling

• 4 large egg yolks (room temperature)
• 1/4 cup cornstarch
• 1/2 cup packed brown sugar
• 3/4 cup real maple syrup
• Pinch kosher salt
• 1 cup chopped toasted pecans (from Step 1)
• 2 teaspoons vanilla extract

In a large pot off the heat, whisk together the egg yolks, cornstarch, and 1 tablespoon water until smooth.

Then whisk in 1/2 cup packed brown sugar, the maple syrup, and a pinch of kosher salt.

Place the pot over medium-high heat and bring to a gentle boil, stirring constantly.

Continue stirring for 5-8 minutes until the mixture thickens noticeably.

Remove from heat, strain through a fine mesh sieve into a heatproof bowl, and stir in about 1 cup of the chopped toasted pecans (from Step 1) and 2 teaspoons vanilla extract.

Cover and chill in the refrigerator until set, about 1 hour.

I recommend tasting the filling at this point and adjusting the salt if needed – a tiny pinch brings out the nutty flavor beautifully.

Step 3: Mix and Bake the Cupcake Batter

• 1 cup melted coconut oil (cooled slightly)
• 1/2 cup bourbon
• 1/2 cup strong black coffee
• 2 large eggs
• 2/3 cup plain Greek yogurt
• 1 cup granulated sugar
• 2 cups all-purpose flour
• 3/4 cup unsweetened cocoa powder
• 1 1/2 teaspoons baking soda
• 3/4 teaspoon kosher salt

Preheat the oven to 350°F again if needed and line 20-22 cupcake molds with paper liners.

In the bowl of a stand mixer (or using a hand-held mixer), beat together the melted coconut oil (cooled slightly), 1/2 cup bourbon, strong black coffee, 2 large eggs, Greek yogurt, and granulated sugar until smooth.

Add in the flour, cocoa powder, baking soda, and 3/4 teaspoon kosher salt.

Mix until you have a smooth batter with no lumps.

Divide the batter evenly among the prepared cupcake liners, filling each about two-thirds full.

Bake for 18-22 minutes until the tops are just set and no longer wiggly in the center.

Remove from the oven and allow the cupcakes to cool before filling.

Step 4: Make and Cool the Frosting Base

• 4 tablespoons salted butter
• 1/2 cup heavy cream
• 1 cup packed brown sugar

In a medium saucepan over medium heat, melt together 4 tablespoons salted butter, the heavy cream, and 1 cup packed brown sugar.

Stir until the butter is melted and the sugar has dissolved.

Bring to a boil and cook for about 1 minute.

Pour the hot mixture into the bowl of a stand mixer (or a large mixing bowl) and refrigerate (or freeze for 15-20 minutes) until cool to the touch.

I like using high-quality butter for extra creamy frosting.

Step 5: Finish the Frosting

• 12 tablespoons salted butter
• 1 tablespoon vanilla extract
• 3 cups powdered sugar (sifted)
• 0.5–1 cup finely chopped toasted pecans (from Step 1)

Retrieve the cooled butter mixture from the fridge or freezer.

Add the remaining 12 tablespoons salted butter, 1 tablespoon vanilla extract, and sifted powdered sugar.

Beat together with an electric mixer until smooth and fluffy.

Gently fold in 1/2 to 1 cup of the finely chopped toasted pecans (from Step 1) to give it texture and flavor.

Step 6: Assemble and Decorate the Cupcakes

• Coled cupcakes (from Step 3)
• Chilled pecan pie filling (from Step 2)
• Pecan frosting (from Step 5)
• Remaining chopped toasted pecans (from Step 1)
• 22 whole pecans (from Step 1)

Once the cupcakes and filling are cooled, use a paring knife to cut a cone-shaped piece out of the center of each cupcake.

Spoon the chilled pecan pie filling (from Step 2) into each hole.

Frost the tops of the cupcakes generously with the prepared pecan frosting (from Step 5).

Sprinkle the remaining chopped pecans (from Step 1) on top and finish each cupcake by placing a whole reserved pecan in the center.

For an extra touch, I sometimes drizzle with a little maple syrup or a pinch of flaky salt.

Ultimate Chocolate Pecan Pie Cupcakes

Delicious Ultimate Chocolate Pecan Pie Cupcakes recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 24 minutes mins

Cook Time 48 minutes mins

Total Time 1 hour hr 12 minutes mins

Servings 4

Calories 7250 kcal

Ingredients

  

For the toasted pecans:

• 3 cups raw pecans
• 1/2 tsp ground cinnamon
• 2 tbsp packed brown sugar
• 2 tbsp bourbon
• 1 tsp vanilla extract

For the pecan pie filling:

• 1/4 cup cornstarch
• 4 large egg yolks (room temperature)
• 2 tsp vanilla extract
• 1/2 cup packed brown sugar
• 3/4 cup real maple syrup (for best flavor)

For the cupcakes:

• 3/4 cup unsweetened cocoa powder
• 1/2 cup strong black coffee
• 2 cups all-purpose flour (I use King Arthur flour)
• 3/4 tsp kosher salt
• 1 cup melted coconut oil (cooled slightly)
• 1/2 cup bourbon
• 1 cup granulated sugar
• 1 1/2 tsp baking soda
• 2 large eggs
• 2/3 cup plain Greek yogurt

For the frosting:

• 1 tbsp vanilla extract
• 12 tbsp salted butter (I prefer Kerrygold for richness)
• 4 tbsp salted butter
• 1/2 cup heavy cream
• 3 cups powdered sugar (sifted)
• 1 cup packed brown sugar

For the topping:

• 22 whole pecans

Instructions

 

• Preheat your oven to 350°F and line a baking sheet with parchment paper. On the sheet, combine the raw pecans, 2 tablespoons bourbon, 1 teaspoon vanilla extract, 2 tablespoons packed brown sugar, and 1/2 teaspoon ground cinnamon. Toss well and bake for 8-10 minutes until the pecans are toasted and aromatic. Once done, sprinkle with sea salt if you wish. Roughly chop the pecans, saving 22 whole pecans for garnishing later.
• In a large pot off the heat, whisk together the egg yolks, cornstarch, and 1 tablespoon water until smooth. Then whisk in 1/2 cup packed brown sugar, the maple syrup, and a pinch of kosher salt. Place the pot over medium-high heat and bring to a gentle boil, stirring constantly. Continue stirring for 5-8 minutes until the mixture thickens noticeably. Remove from heat, strain through a fine mesh sieve into a heatproof bowl, and stir in about 1 cup of the chopped toasted pecans (from Step 1) and 2 teaspoons vanilla extract. Cover and chill in the refrigerator until set, about 1 hour. I recommend tasting the filling at this point and adjusting the salt if needed – a tiny pinch brings out the nutty flavor beautifully.
• Preheat the oven to 350°F again if needed and line 20-22 cupcake molds with paper liners. In the bowl of a stand mixer (or using a hand-held mixer), beat together the melted coconut oil (cooled slightly), 1/2 cup bourbon, strong black coffee, 2 large eggs, Greek yogurt, and granulated sugar until smooth. Add in the flour, cocoa powder, baking soda, and 3/4 teaspoon kosher salt. Mix until you have a smooth batter with no lumps. Divide the batter evenly among the prepared cupcake liners, filling each about two-thirds full. Bake for 18-22 minutes until the tops are just set and no longer wiggly in the center. Remove from the oven and allow the cupcakes to cool before filling.
• In a medium saucepan over medium heat, melt together 4 tablespoons salted butter, the heavy cream, and 1 cup packed brown sugar. Stir until the butter is melted and the sugar has dissolved. Bring to a boil and cook for about 1 minute. Pour the hot mixture into the bowl of a stand mixer (or a large mixing bowl) and refrigerate (or freeze for 15-20 minutes) until cool to the touch. I like using high-quality butter for extra creamy frosting.
• Retrieve the cooled butter mixture from the fridge or freezer. Add the remaining 12 tablespoons salted butter, 1 tablespoon vanilla extract, and sifted powdered sugar. Beat together with an electric mixer until smooth and fluffy. Gently fold in 1/2 to 1 cup of the finely chopped toasted pecans (from Step 1) to give it texture and flavor.
• Once the cupcakes and filling are cooled, use a paring knife to cut a cone-shaped piece out of the center of each cupcake. Spoon the chilled pecan pie filling (from Step 2) into each hole. Frost the tops of the cupcakes generously with the prepared pecan frosting (from Step 5). Sprinkle the remaining chopped pecans (from Step 1) on top and finish each cupcake by placing a whole reserved pecan in the center. For an extra touch, I sometimes drizzle with a little maple syrup or a pinch of flaky salt.