Chocolate Caramel Cupcakes are rich, moist chocolate cupcakes filled with homemade salted caramel and topped with fluffy whipped chocolate ganache. Add a caramel drizzle and flaky sea salt for the ultimate caramel-filled chocolate cupcake.

There are chocolate cupcakes, and then there are chocolate cupcakes with a gooey salted caramel center hiding inside.

And if we’re putting caramel inside a chocolate cupcake, we might as well go all in. There’s more chocolate in the whipped ganache on top, another drizzle of salted caramel, and a sprinkle of flaky sea salt.

The whipped ganache is especially important here because it’s lighter and less sweet than chocolate buttercream, which is exactly what these caramel-filled cupcakes need.

For September’s Cupcake of the Month, I wanted to lean into fall flavors without pulling out the pumpkin just yet. Salted caramel felt like the perfect place to start, especially when it’s stuffed inside a chocolate cupcake and paired with even more chocolate on top.

Ingredients and Substitutions

The full ingredient amounts are listed in the recipe card below, but here are a few notes about the most important ingredients and possible substitutions.

Natural Unsweetened Cocoa Powder

This recipe is developed with natural cocoa powder, which is acidic and works with the baking soda to help the cupcakes rise. Stick with natural cocoa rather than Dutch-process cocoa for this recipe. Use a high-quality cocoa powderhttps://amzn.to/3lPr2xJ for the best texture and flavor.

Hot Coffee

Coffee makes chocolate taste more intensely chocolatey without making the cupcakes taste like coffee. If you don’t have coffee or prefer not to use it, substitute an equal amount of hot water, as the hot liquid helps the cocoa powder bloom.

Buttermilk

The acidity in buttermilk reacts with the baking soda while also contributing to a soft, tender crumb. For the best results, use real cultured buttermilk rather than regular milk. If a substiution is necessary, add 1½ teaspoons of lemon juice or vinegar to 113 grams of whole milk and let it sit for 5 to 10 minutes before using.

Salted Caramel Sauce

I use my homemade salted caramel sauce for both filling the cupcakes and drizzling over the frosting. A thick store-bought caramel sauce also works, but avoid thin caramel syrup, which will soak into the cupcake instead of forming a gooey center.

Semisweet Chocolate

Use a good-quality semisweet chocolate bar, around 55 to 60% cacao, rather than chocolate chips for the whipped ganache. Bar chocolate melts more smoothly, as the stabilizers in chocolate chips can affect the texture of the ganache.

All-Purpose Flour

Regular all-purpose flour gives these cupcakes their soft, tender crumb. A 1:1 gluten-free baking flour can be used to keep the cupcakes gluten free.

How to Make Chocolate Caramel Cupcakes

There are three parts to these cupcakes: the chocolate cupcakes, the salted caramel filling, and the whipped chocolate ganache. The cupcakes and ganache both need time to cool, so you can make the caramel ahead of time or while the cupcakes are cooling.

Make the Chocolate Cupcakes

Whisk together the flour, sugar, cocoa powder, baking powder, baking soda, and salt. In a separate bowl, whisk the egg, buttermilk, vegetable oil, and vanilla extract. Pour the wet ingredients into the dry ingredients and mix until just combined. At this point, the batter will be quite thick. Slowly pour in the hot coffee and whisk until smooth. The coffee thins the batter considerably, so don’t worry when it looks much thinner than a typical cupcake batter.

Divide the batter evenly among 12 lined muffin cups, filling each about three-quarters full. Bake at 350°F for 18 to 20 minutes, until a toothpick inserted into the center comes out with a few moist crumbs. Cool completely before filling.

Make the Chocolate Ganache

Place the chopped chocolate in a heatproof bowl. Heat the heavy cream until it is steaming and just beginning to simmer around the edges, then pour it over the chocolate. Let it sit undisturbed for 2 to 3 minutes to give the hot cream time to melt the chocolate, then stir slowly until the chocolate and cream come together into a completely smooth, glossy ganache. Stir in the vanilla extract and salt. Refrigerate the ganache until it is completely cool and thickened but still soft enough to scoop.

Using an electric mixer, whip the cooled ganache until it becomes noticeably lighter in color and fluffy enough to hold stiff peaks. Stop mixing as soon as it reaches this point. Overwhipping can make the ganache grainy.

Fill and Frost the Cupcakes

Use a cupcake corer, large piping tip, or small paring knife to remove the center of each completely cooled cupcake, cutting about halfway to two-thirds of the way down. Don’t cut all the way through the bottom. Fill each cavity nearly to the top with salted caramel sauce. Pipe the whipped chocolate ganache over each cupcake. Finish with another drizzle of salted caramel sauce and a sprinkle of flaky sea salt, if desired.

Whipped Ganache Frosting

Whipped ganache looks deceptively simple: chocolate, cream, and a mixer. But there’s a reason we need to pay careful attention when we’re whipping it.

Kitchen Chemistry

Ganache is an emulsion, with microscopic droplets of fat and water held together in a stable mixture. Whipping adds air to that emulsion, but too much agitation can destabilize it.

When hot cream is mixed with chocolate, the water in the cream and the cocoa butter in the chocolate form a smooth emulsion. As the ganache cools, the cocoa butter begins to crystallize, thickening the mixture enough to trap air when it’s whipped.

That trapped air is what turns dense ganache into a lighter, fluffy frosting. But keep whipping and the fat droplets can start to join back together, breaking down the emulsion and leaving the ganache grainy or greasy instead of silky.

Stop as soon as the ganache lightens in color and holds stiff peaks. At that point, it has enough structure to pipe onto the cupcakes without losing the smooth texture we want.

Frequently Asked Questions

Can I make the cupcakes ahead of time?

Yes. The chocolate cupcakes can be baked a day ahead and stored in an airtight container at room temperature. You can also make the salted caramel sauce ahead of time. I recommend waiting to fill and frost the cupcakes until the day you plan to serve them for the best texture.

Can I use store-bought caramel?

Yes, as long as it is thick enough to stay inside the cupcake. Look for a thick caramel sauce rather than a thin caramel syrup, which can soak into the cake instead of creating a distinct caramel center.

Why is my whipped ganache grainy?

Whipped ganache can become grainy if it is overwhipped or if the ganache was not completely emulsified before chilling. Make sure the chocolate is fully melted and the ganache is smooth before refrigerating, then stop whipping as soon as it becomes lighter in color and holds stiff peaks.

Can I use chocolate chips for the ganache?

A chopped semisweet chocolate bar is the best choice. Chocolate chips contain stabilizers that help them hold their shape during baking, which can make the ganache less smooth. If chocolate chips are all you have, they can work, but the texture may not be quite as silky.

Help! My caramel is too runny. What should I do?

If your caramel is only a little softer than you’d like, fill the cupcakes and transfer them to the refrigerator. Homemade caramel thickens as it chills, which will help keep the filling in place. Store the filled cupcakes in the refrigerator until you’re ready to serve them. If the caramel is very thin or watery, chill the sauce before filling the cupcakes. If it still doesn’t thicken enough, it may need to be cooked a little longer before using.

More Caramel Recipes

• Chocolate Caramel Cake
• Caramel Apple Cake
• Caramel Pecan Turtle Brownies
• Caramel Apple Cheesecake
• Caramel Buttercream Frosting
• Salted Caramel Pumpkin Bread

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