These decadent chocolate filled cupcakes are stuffed with a creamy chocolate ganache and then topped with a rich chocolate buttercream. They are light and fluffy and are a chocolate lovers dream! These cupcakes are the perfect cupcake to make for any party or brunch!

Chocolate cupcakes topped with chocolate buttercream aligned on a blue gray backdrop
You can use any chocolate frosting to top these ganache filled cupcakes.

What’s better than a rich and decadent chocolate cupcake? A chocolate cupcake that has a ganache filling in the middle!

These cupcakes are seriously so easy to make. The recipe makes 12 cupcakes that are perfect for adding a chocolate ganache filling. You can top these with a homemade chocolate ganache frosting , a light whipped chocolate frosting, or a classic chocolate buttercream frosting like I did here.

In pastry school, we would try to come up with crazy flavor combos for our desserts, but I really think that classic chocolate is the way to go. It is such a people pleaser, no one can say no to it!

Like my 6 inch chocolate cake and my one bowl chocolate cake, this recipe makes a fluffy yet moist chocolate cupcake. What makes it special is that we are adding in a creamy and silky smooth ganache filling. Looking for something a little more indulgent? Check out these chocolate fudge cupcakes!

f you like other filled cupcakes, try my chocolate raspberry filled cupcakes too!

Ingredients needed

  • Granulated Sugar
  • All purpose flour
  • Cocoa powder (unsweetened)
  • Baking soda
  • Baking powder
  • Kosher Salt
  • Just one egg
  • Vanilla Extract
  • Whole milk yogurt – you can substitute greek or even sour cream
  • Warm black coffee- this is brewed black coffee (instant or not!)
  • Vegetable oil
  • Semi sweet dark chocolate (either chips or chopped small)
  • Heavy cream

How to make this recipe

Make the cupcakes

  1. Start my making the cupcakes. Preheat the oven to 350° F and in the bowl of a hand or stand mixer add the sugar, flour, cocoa, baking soda, baking powder, and kosher salt. Whisk to combine.
  2. Next add in the one egg, vanilla extract, yogurt, warm coffee, and vegetable oil. Mix on low speed working your way up to medium for 2 minutes until thoroughly combined.
  3. Line a 12 cup muffin tin with liners and fill 2/3 of the way up.
  4. Bake for 18 mins

Make the ganache filling

To get the consistency right for the ganache you are going to use a 2:1 ratio.

2 parts chocolate to 1 part cream.

This creates a truffle like filling that makes it easy to scoop. Make sure you are either using chocolate chips, or chopping up your chocolate to make it easier to melt.

  1. Pour the chocolate into a small bowl.
  2. Heat the cream in the microwave 15-30 seconds at a time just until scalding hot.
  3. Pour the cream over the chocolate but do not stir.
  4. Wait 5 minutes, then stir with a spatula to combine.
  5. Refrigerate the ganache for 20 minutes so that it hardens a bit.

Chocolate Ganache Filling tips

  • The ganache will not be ready to use as filling right away, you need to refrigerate it to let it harden up a little.
  • In pastry school they told us not to use a whisk to stir ganache but to use a spatula instead. Mixing with a whisk can create bubbles in your ganache, and you want to keep it as smooth as possible. Use a spatula instead.
  • If the ganache is too hard to scoop, microwave it for 10-15 seconds at a time, stirring in between, to get it to the right consistency for filling.
  • You want the filling to be like the consistency of toothpaste.

How to fill the inside of cupcakes

To fill the cupcakes you can either use a cupcake corer or an apple corer.

I don’t have either of those (LOL) so I just use a small pairing knife to cut a small quarter sized hole that is 1/2 inch deep, at the top of the cupcake and lift it off.

Remember to save the tops though! Don’t throw them out! You will be putting them back on after the cupcake is filled.

Then using a tsp, scoop the ganache and add it to the hole you made in the cupcake. Put the top back on and press down. Who cares if it doesn’t look the prettiest right now, because you are topping it with buttercream anyways!

Topping the cupcakes

To top the cupcakes, make this easy chocolate buttercream. You can either pipe them on like I did here using a Atecco 855 tip, or just slather it on with an offset spatula or spoon!

Chocolate filled cupcakes on a cooling rack with its wrapper undone
These are light and fluffy!

Recipe FAQ

  1. Can I fill the cupcake before baking? For this recipe, no. To get the best results, you need to fill the cupcake after it’s baked. If you prefer to make a cupcake that is filled before baking, try my red velvet cheesecake cupcakes
  2. Can I fill this cupcake with buttercream instead? Of course! You totally can, follow the same steps above.
  3. Can I make this recipe ahead? Also yes! Make the cupcakes and store them in an airtight container for up to 3 days. Make the chocolate ganache and store it in the fridge, up to a week in advance. When you are ready to fill, microwave the ganache for 15 seconds and stir to bring it to a better filling consistency.
  4. How do I store the cupcakes? Once filled and frosted, you can keep them under a cake dome or in a 9×13 inch dish covered with plastic wrap for up to 5 days. There is no need to refrigerate.
  5. Can these be frozen? You can freeze the cupcakes. After they have cooled, place them in a freezer safe zip top bag and freeze for up to 3 months. Defrost, fill and decorate as above. I do not recommend freezing the ganache.
  6. How high should I fill the cupcake liners? Make sure to only fill them 2/3 of the way up. Otherwise they will overflow when they are baking, and you might also not have enough batter for 12 cupcakes.
A chocolate cupcake filled with chocolate ganache cut in half to reveal the inside.
Surprise! Theres decadent chocolate ganache inside!
Chocolate filled cupcakes on a cooling rack with its wrapper undone
5 stars (5 ratings)

Chocolate Filled Cupcakes with Ganache Filling

These decadent chocolate filled cupcakes are stuffed with a creamy chocolate ganache and then topped with a rich chocolate buttercream. They are light and fluffy and are a chocolate lovers dream! These cupcakes are the perfect cupcake to make for any party or brunch!


Chocolate Cupcakes

  • 3/4 cup granulated sugar
  • 2/3 cup all purpose flour
  • 1/3 cup cocoa powder
  • 1/2 tsp baking soda
  • 1/4 tsp baking powder
  • 1/4 tsp kosher salt
  • 1 egg, large
  • 1/2 tsp vanilla extract
  • 1/3 cup whole milk yogurt
  • 1/3 cup black coffee, warm or cold
  • 1/8 cup vegetable oil

Chocolate Ganache Filling

  • 4 oz chopped chocolate, semi sweet
  • 1/4 cup heavy cream


Make the cupcakes

  • Preheat the oven to 350° F and line a 12 cup muffin tin with cupcake liners, set aside.
  • Dry ingredients whisked together in a mixing bowl
    In a bowl of a hand or stand mixer fitted with the paddle attachment, combine the 3/4 cup sugar, 2/3 cup flour, 1/3 cup cocoa, 1/2 tsp baking soda, 1/4 tsp baking powder, and 1/4 tsp kosher salt. Whisk lightly or mix on low to combine.
  • Add the 1 egg, 1/2 tsp vanilla extract 1/3 cup whole milk yogurt, 1/3 cup black coffee, and 1/8 cup vegetable oil and mix on low speed working up to medium as it combines. Mix for 2 minutes on medium speed.
  • A muffin tin lined with chocolate cupcake batter
    Fill the cupcake liners 2/3rd of the way full. Bake for 18 minutes or until the tops of the cupcakes bounce back when lightly pressed.

Make the chocolate ganache filling

  • Chocolate and cream in a glass bowl on a blue surface
    In a small bowl, add the 4 oz chopped chocolate. Heat the cream in the microwave for 15-30 seconds at a time until scalding. Pour the cream over the chocolate and let sit for 5 minutes. DO NOT stir right away.
  • Chocolate ganache melted in a glass bowl
    Stir with a spatula after 5 mins until smooth.
  • Hardened chocolate ganache ready to fill cupcakes in a glass bowl with spoon
    Refrigerate the ganache for 20 minutes to harden.

Fill the cupcakes

  • A chocolate cupcake with a hole on it's top with a knife next to it on a blue surface
    Use a cupcake corer or a small knife, cut a 1/2 inch deep hole about the size of a quarter and lift the top off, saving it for after.
  • chocolate cupcakes filled with ganache in a 12 pan cupcake tin
    Fill the cupcake using a teaspoon of ganache and place the top of the cupcake back on. Press lightly, then top with buttercream frosting! (See notes below for frosting recipe)


Here’s my chocolate buttercream recipe to use to top the cupcakes. You can also frost with a chocolate ganache frosting or a light whipped chocolate frosting.
Make sure to only fill the cupcake liners 2/3 of the way full. If you fill them too high they will overflow and you may not have enough to make 12 cupcakes. 
Serving: 1cupcake, Calories: 154kcal, Carbohydrates: 25g, Protein: 2g, Fat: 6g, Saturated Fat: 4g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 2g, Trans Fat: 1g, Cholesterol: 21mg, Sodium: 116mg, Potassium: 94mg, Fiber: 2g, Sugar: 18g, Vitamin A: 99IU, Vitamin C: 1mg, Calcium: 25mg, Iron: 1mg
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