Ultimate Chocolate Cupcakes with Ganache Filling

My husband’s birthday is always celebrated with a big chocolate cake.  This year though I convinced him that cupcakes would be even better – I am not sure how I managed that one, but I did.  I saw this chocolate cupcake recipe in Cook’s Illustrated that looked so amazing, I just had to make them.  They were filled cupcakes, and filled with ganache – but the best thing about this recipe is that all you did was put a dollop of ganache on top of the cupcake batter, and magically the batter bakes around it – forming a filling. Well, I just had to give it a try – and use my husband’s birthday as the excuse.

I have to say, this ganache was something else – I wanted to just eat it plain…it was so rich and creamy – and incredibly smooth – it just melted in your mouth immediately.  I was getting very excited to try the finished product.  Ok, my husband likes his food, but he does have a discerning palate – he doesn’t just settle for anything.  He took and bite and told me they were the best cupcakes he has ever eaten in his life.  From him, that is huge.  We have had some pretty incredible cupcakes in our lives – but these were just ridiculously moist – the ganache didn’t stay in one piece, it basically melted all over the center of the cake to make an even more intense moist chocolately center.  Oh my.  The frosting was pretty incredible as well – not too sweet, but nice and rich – and oh so smooth.

Well, at least I beat last year, but how am I going to top this one?


Ganache Filling:

  • 2 ounces bittersweet chocolate, chopped fine
  • ¼ cup heavy cream
  • 1 tablespoon confectioners’ sugar

Chocolate Cupcakes:

  • 3 ounces bittersweet chocolate, chopped fine
  • 1/3 cup (1 ounce) Dutch-processed cocoa
  • ¾ cup hot coffee
  • ¾ cup (4 1/8 ounces) bread flour
  • ¾ cup (5¼ ounces) granulated sugar
  • ½ teaspoon table salt
  • ½ teaspoon baking soda
  • 6 tablespoons vegetable oil
  • 2 large eggs
  • 2 teaspoons white vinegar
  • 1 teaspoon vanilla extract


  • 1/3 cup (2 1/3 ounces) granulated sugar
  • 2 large egg whites
  • Pinch table salt
  • 12 tablespoons (11/2 sticks) unsalted butter, softened and cut into 1-tablespoon pieces
  • 6 ounces bittersweet chocolate, melted and cooled
  • 1/2 teaspoon vanilla extract


Ganache Filling:

Place-chocolate, cream, and confectioners’ sugar in medium -microwave-safe bowl. Heat
in microwave on high power until mixture is warm to touch, 20 to 30 seconds.
Whisk until smooth; transfer bowl to refrigerator and let stand until just
chilled, no longer than 30 minutes.

Chocolate Cupcakes:

Adjust oven rack to middle position and heat oven to 350 degrees. Line standard-sized muffin pan
(cups have ½-cup capacity) with baking-cup liners. Place chocolate and cocoa in medium bowl. Pour hot coffee over mixture and whisk until smooth. Set in refrigerator to cool completely, about 20 minutes. Whisk flour, sugar, salt, and baking soda together in medium bowl; set aside.

Whisk oil, eggs, vinegar, and vanilla into cooled chocolate-cocoa mixture until smooth. Add flour mixture and whisk until smooth.

Divide batter evenly among muffin pan cups. Place one slightly rounded teaspoon ganache filling on top of each cupcake. Bake until cupcakes are set and just firm to touch, 17 to 19 minutes. Cool cupcakes in muffin pan on wire rack until cool enough to handle, about 10 minutes. Carefully lift each cupcake from muffin pan and set on wire rack. Cool to room temperature before frosting, about 1 hour.


Combine sugar, egg whites, and salt in bowl of stand mixer; place bowl over pan of simmering water. Whisking gently but constantly, heat mixture until slightly thickened, foamy, and registers 150 degrees on instant-read thermometer, 2 to 3 minutes.

Place bowl in stand mixer fitted with whisk attachment. Beat mixture on medium speed until consistency of shaving cream and slightly cooled, 1 to 2 minutes. Add butter, 1 piece at a time, until smooth and creamy. (Frosting may look curdled after half of butter has been added; it will smooth with additional butter.) Once all butter is added, add cooled melted chocolate and vanilla; mix until combined. Increase
speed to medium-high and beat until light, fluffy, and thoroughly combined, about 30 seconds, scraping beater and sides of bowl with rubber spatula as necessary.

To frost, mound 2 to 3 tablespoons frosting on center of each cupcake. Using small icing spatula or butter knife, spread frosting to edge of cupcake, leaving slight mound in center.

For a printer-friendly version of this recipe, please click here:  Ultimate Chocolate Cupcakes with Ganache Filling

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61 thoughts on “Ultimate Chocolate Cupcakes with Ganache Filling

    1. I didn’t mean to put that, but, since I did at first – I will remind everyone to use the best quality chocolate you can – I usually use the blocks of bulk chocolate they sell at Whole Foods – I am not sure of the brand, but it is excellent.

  1. These are beautiful – as always! Your cupcakes are just amazing looking. I have no doubt you’ll find a way to top these for hubby’s next birthday. ;) I could never pull these off, so I’m just going to have to live vicariously this time!

  2. I’ve had this recipe marked in my Cooks Illustrated forever, but I have a favorite choc cupcake recipe that I’m always drawn to that has the best chocolate fudge icing every! It’s posted on my site, but after reading your comments about this cupcake, I may have to finally give them a try.

  3. amazing! i can never get enough ganache and usually i don’t LOVE cupcakes due to the “dry” factor as well. so these are a must!!

  4. Chocolate is a flavor that can be found in almost any food and in many drinks. These chocolate cocktails are treats for your taste buds with some being more …


  5. Thank u so much for posting this! I found u by way of food gawker over the weekend and had to try them! Absolutely delicious. I haven’t iced them yet but I did notice that my icing didn’t hold up as nicely as ur’s. I’m not much of a baker but am I to assume this is due to “over softened” butter(?) or what would u suggest?

    Also, I love the recipe layout and comments section. What widgets/plugins do u use, if u don’t mind. Once I get the cupcakes on my site, I’ll definitely give u a shout out! Peace n blessings! Zina

    1. I actually think it was probably the egg whites – that is the tricky part fo the frosting, and you need to whip them just enough so they stay firm. I would chill the frosting and maybe whipping it one more time before frosting, that might work.

      I actually don’t use any widgets for the recipe or comments section, it just comes with the theme I chose from wordpress. But thanks, glad you like it!!

    1. I get it in bulk at Whole Foods, but you should be able to find bittersweet chocolate in any supert market in the baking section. Feel free to substitute dutch-pressed cocoa for any type of unsweetened cocoa, it should be fine.

  6. ¾ cup (4 1/8 ounces) bread flour

    is it 3/4 cup and 4 1/8 ounces of bead flour or
    is it 3/4 cup or 4 1/8 ounces?

  7. Okay Dawn–another question :) I plan to make these tonight and frost them with buttercream tomorrow. Should I refrigerate overnight or are they fine at room temperature? Once frosted how should I store them? Appreciate your help—I am not a cupcake expert!!

    1. Hi Natalie – I would just keep them covered overnight – do not refrigerate. I have a big tupperware container that I store cupcakes in the pantry. If you don’t have something like that, use a deep baking dish, or something that you can cover without touching the frosting. Good luck, and let me know how they turn out!!

  8. I found this recipe and am excited to try. I haven’t baked a lot but am beginning to do so. I have a couple of questions…..I think you said it didn’t matter if Dutch processed cocoa was used or regular cocoa however, in other recipes I understand it is recommended to use baking powder when you use Dutch processed cocoa. This recipe does not call for baking powder but everyone seems to have had no problems. Also, do I need to adjust anything if I live at 6,000 feet? THANK YOU.

  9. I musta done something wrong. :( I made it and all the ganache sank to the bottom. Very good still though!!

  10. I hate the taste of coffee, I want to make these for my sister-in-law’s baby shower, do they taste strongly of coffee? Is it a necessary ingredient?

    1. Hi Kelly, it doesn’t taste at all like coffee, you would never know it was in there. If you are still worried though, you could probably substitute hot chocolate (made with water) instead. You do need to have the liquid ingredient. Good light!!

  11. I think someone used this recipe and put a raspberry on top of each cupcake they brought to my house. I thought they must have bought them at a bakery! They were awesome!

  12. These cupcakes were AMAZING!! I was surprised at how well they turned out and how easy they were to whip up. I added 1/2 tsp. almond extract (as well as the vanilla) and 3/4 C. powdered sugar to the frosting at the end.

  13. I’m wondering if it would be possible to substitute the bittersweet chocolate in the frosting for pea it butter to make a peanut butter frosting?would peanut butter be too creamy?

  14. I’m planning to use the ganash recipe but with box cake.. will that be ok? I’m not much of a baker… :P

      1. I used Ghiradelli bittersweet chocolate. I have since read others comments who said the ganache sank to the bottom. If I ever make this again, I will bake the cupcakes, let them cool and put a layer of ganache on top prior to frosting. BTW, everyone loved these cupcakes.

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