Gooey Filled Chocolate Cupcakes, Gluten Free

Guess what? This is National Chocolate Cupcake Day.  The whole day!

In honor of National Chocolate Cupcake Day (2011) we are celebrating with a homemade gluten-free creation of that infamous (hello: Hostess) gooey filled chocolate cupcake treat.

I’m a big Hostess Cupcake fan from way back.  Or more a fan of the concept of a Hostess Cupcake – a creamy gooey filled chocolate baby-cake topped with a chocolate frosted finish.  

Whenever my mom took me grocery shopping a hundred or so years ago,  put-putting there in her old Ford Falcon I’d spend most of the time communing with the Hostess Cupcake stack located on aisle 7 next to the Twinkies and Sno Balls. Hostess anything never came home with us – my mom was a baker extraordinaire and those things were expensive for a family with four kids, three of them hollow-legged boys.

By the time I had earned enough babysitting money to buy a package I learned a really good lesson. The anticipation (and the packaging) is sometimes way better than the thing inside. Hostess Cupcakes were salty, the cake a little bit dry, and there was  faint metallic taste like what new braces taste like – in the gooey filling. I was as sad as could be.

Every once in a while after that I’d buy a package hoping they’d changed the recipe or that my tastes had evolved. That never happened.  I envied the kids who brought Hostess Cupcakes in their school lunches and ate them with gusto. I even envied the kids who thought Twinkies were gourmet treats.

We ate homemade goodies in our house, and while not one of them rose to the dressiness of a Hostess Cupcake, the stuff was hands down better tasting. If my mom made chocolate cupcakes, they were tiny things and plain but tasty. There were always just enough to go around and I never got a 2nd one.  If they were frosted, it would be with a thin, almost transparent layer of icing like she was stretching a one-quarter recipe to fit 12 cupcakes. While my mom truly rocked the cookie and brownie universe, cakes were just not her thing.

When I got to be an adult with my own kitchen and I could buy as many Hostess Cupcakes as I wanted, I rarely did. When we had kids we never brought them into the house for the same reason most parents avoid that stuff – too much sugar and not enough food value. Even a Oreo had more standing than the lowly Hostess Cupcake. I learned to make decent cupcakes but never ever considered that I could make a homemade version of a Hostess Cupcake.

That is, until I was living gluten-free, almost dairy-free, kid-free and had to seriously watch my sugar intake.  Yep. Then I learned the art of making gooey ridiculous over-the-top treats.

I learned to bake because I had the time, finally. The ingredients, like chocolate chips, didn’t keep disappearing into the backpacks of children,  and the stress of endless last-minute PTA bake sales were behind me.  My only challenge was learning the gluten-free redux of everything we loved. And remembering to reuse the ganache instead of making more – I think there might be 35 pounds in the refrigerator stored in various containers that lurk everywhere.

This gooey filled chocolate gluten-free cupcake is a slightly modified version of a simple but delicious chocolate cupcake from Alice Medrich and Scharffen Berger chocolate. That recipe is  here.  The filling is slightly modified from a recipe by Nicole Kaplan (here) and also in the Marshmallow Fluff Cookbook which I was able to score from a used bookstore in Berkeley.  The ganache is my go-to version from Ina Garten here that I use frequently.

Kitchen Tip: If you have a big giant mixer like I do, and you are making a small batch – be sure to use the silicone spatula to do a final sweep to pick up all the rogue ingredients that often get stuck in the bottom of a small batch/large mixer set-up.  Nothing like pouring out the batter to find half of it stuck on the bottom to make for a certain baking wreck.

These treats take little time to put together considering they have three parts – cake, filling and topping. And they keep rather well in the refrigerator. Just bring to room temperature before serving if you can wait that long. And as usual, chocolate gets better with a little aging, so you can make the cupcakes one day and fill/frost the next and the whole thing will be less effort and is guaranteed to taste sublime.

These are not those old Hostess Cupcakes and they don’t pretend to be. They are better.

Gooey Filled Chocolate Cupcakes, Gluten Free
Adapted from Alice Medrich (cupcakes) Nicole Kaplan (filling) and Ina Garten (ganache)
  • 4.5 oz. GF flour (about 1 cup) (3 oz. superfine brown rice flour, 1 oz. superfine white rice flour 0.5 oz. tapioca starch)
  • 7.5 oz. white sugar (about 1 heaping cup)
  • 1.5 oz. (about ⅓ heaping cup) Scharffen Berger unsweetened cocoa (or your favorite)
  • ½ teaspoon very fine powdered instant espresso
  • ½ teaspoon baking soda
  • pinch kosher salt
  • 4 oz. (1 stick) unsalted butter, melted and slightly cooled
  • 2 large eggs, room temperature
  • ½ teaspoon vanilla
  • ½ teaspoon creme de cacao
  • 3.75 oz. hot water (about ½ cup)
  • 10 oz. powdered sugar, sifted (about 2.5 cups)
  • 3 oz. unsalted butter, room temperature (about 6 tablespoons)
  • 6-7 oz. Marshmallow Fluff (not marshmallow cream)
  • 1-2 tablespoons heavy cream
  • 4 oz. heavy cream (about ½ cup)
  • 8 oz. semisweet chocolate chopped (not chocolate chips!)
  1. Preheat oven to 325. Line one cupcake tin (12) with grease proof paper liners.
  2. In a stand mixer bowl weigh flour, sugar, cocoa, and add in espresso, baking soda, salt and mix thoroughly. Add the eggs and flavorings to the melted butter and stir. Pour into stand mixer and with a paddle attachment, mix for a minute. Scrape down sides. Pour in half the hot water and mix again for a minute. Pour in the remaining water and mix for one more minute. Using a spatula, scrape up all the rogue bits and make sure everything is incorporated. Scoop into the cupcake liners evenly. Bake about 12 minutes and rotate. Bake about 8-10 minutes more or just until a toothpick comes out cleanly. Cool and remove the cupcakes to a rack to cool completely.
  1. Weigh the ingredients into a stand mixer bowl. Using a whip attachment, whip for about 2 minutes until incorporated well. Scrape down sides and whip on medium high for about 4 minutes until very fluffy.
  2. Core cupcakes using a knife or a cupcake core thingy. Pipe or spoon in filling neatly and replace with the cupcake core. You may want to cut off some of the stem to make room for the filling because you want the tops to be flush with the rest of the cupcake dome. Let sit for a bit while you make the ganache.
  1. Heat cream in a small saucepan (big enough to dunk the cupcakes in upside down) just until tiny bubbles form and it is steamy hot but not boiling. Add the chopped chocolate and just let the mixture sit for about 3-4 minutes without touching it. Then stir until the chocolate and cream are mixed well. Let the ganache cool slightly before dipping. Sometimes I do a double dip letting the first dip start to set and then I dip again to make the coating thicker. You don't want the ridges of the cutout to show if you can help it - but it won't detract from the taste at all!
  2. Decorate with some leftover filling by placing it in a small piping bag and twirling a design on top. Or pipe a tiny flour on top, or add sprinkles or nothing at all. Do it your way!
  3. And eat!



  1. Absolutely beautiful cupcakes, Lisa! Wow! Now I have a strong hankering for some of these. *sigh* Guess there is only one way to get rid of that urge! 😉

    • GlutenFreeCanteen says:

      Seriously – they are fast and easy. The cupcakes go together in a minute and the only reason it takes any time at all is because you have to let them cool before filling – enjoy!

  2. AHHHH! these are fantastic and beautiful..and i want to gobble them up!!!! lovely pictures also!!

  3. My favorite was always to eat the ganache first and the cupcake second. The same way I ate Snoballs. I MUST make some of those, less the chemical pink coloring. Great job. Thanks.

  4. YUM! Can’t believe these are gluten-free!

  5. Hi Lisa, Your Gooey Filled Chocolate Cupcakes recipe has been selected to be featured in a Recipe Guessing Game. Please share the following link with your friends and fans. To play, go here: Congrats again!! 🙂

  6. Hi Lisa, Stumbled across you recipe and decided to give it a try. I’ve attempted a few gluten free cake/cupcake recipes and this is by far the best. Made two batches this weekend, love love love them! Friends did too. All agree one of the best cupcakes they ever had!

  7. Perfect recipe! 🙂 My family is devouring them right now!

  8. Thank you sooo much!! Your website is amazing! I regularly bake cupcakes and cookies for friends, but one friend always seems to get left out because of a Gluten and Wheat allergy because I never found a recipe I was happy with to make him some cupcakes. If it doesn’t taste right to me I will never give it to someone else. These cupcakes are amazing! It’s his 78th birthday soon and I was despairing about finding something to bake for him. This is the perfect recipe for some birthday cupcakes!

    • GlutenFreeCanteen says:

      So glad! I agree that GF should taste as good or better! Hope your friend has a wonderful birthday.

      • Just an update. My friend LOVED the cupcakes. He hasn’t been able to eat them for round 10 years other than the icky ones you buy in the store, so he gave up buying them. I couldn’t find the marshmallow fluff in store here so I made my own and filled them with that and had a bit of a disaster with the ganache (ganache and me dont mix well) so I whipped up some chocolate buttercream and added a splash of Creme de Cacao for a bit of a kick. His non GF family couldn’t tell the difference! He was so happy to be able to eat cupcakes again at the grand old age of 78.

      • GlutenFreeCanteen says:

        So glad he liked them. And I have disasters all the time. Buttercream is a good rescue, espc with a little liqueur kick. Good thinking!

  9. how much stevia do you use instead of the sugar in these recipies?

    • GlutenFreeCanteen says:

      Loretta, hi. I’m sorry to tell you I have no idea. I am not a stevia or agave user. But perhaps another reader might know.

  10. I made these over the weekend for a game-night at a friend’s house. NO ONE knew they were gluten-free until they saw me eating one. These are by far the most delicious gluten-free cupcakes I’ve ever had. The only change I made was swapping Kahlua for the creme de cacao since I had it on hand.

  11. Jennifer says:

    These are the most amazing cupcakes can’t even tell they are gluten free most others taste kind of gritty or dense. I love these cupcakes read the reciepe last week and already made them twice lol

  12. Ive made these and they are absolutely delicious! My only problem is that they sometimes sink quite a lot in the middle. Any tips on how to keep this from happening? Thanks!

    • GlutenFreeCanteen says:

      Hi Hanna – I fill them a generous 2/3 full. Also, might want to get a thermometer to check the oven temp – too hot or not hot enough can make a difference. Hope that helps.

  13. Help, i’m not sure what marshmallow fluff is. Is there a recipe for it? These look fabulous!

  14. Didn’t have time to order so ended up finding a recipe for homemade fluff. Made these for Valentines Day. The process took a bit longer but they are really good. Next time I won’t double dip the ganache…it’s just a bit too much.

    • GlutenFreeCanteen says:

      Good point about the double dip ganache. I agree. I tend to do it more then the first pass was a little too thin or if the indent where the filling went is deep but yes, it can get thick as it cools. Glad you enjoyed them.


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