Gluten Free Black Bottom Cupcakes

gluten free black bottom cupcakes in pan


Do you know the history of black bottom cupcakes? I certainly didn’t when I set out to create gluten free black bottom cupcakes, and honestly, I don’t really know anything more about them now, except that they’re darned delicious.

gluten free black bottom cupcake with fork

Everyone agrees that they’ve been around for ages, in one incarnation or another.

A chocolate cupcake topped with cream cheese deliciousness that’s hard to beat, as far as a well-rounded sweet treat is concerned.

gluten free black bottom cupcake on paper

Of course the obvious answer to the question of origin is that these scrumptious mini cakes are black on the bottom and white on top (using those colors broadly, as they’re actually brown and cream colored, but who’s counting?).

And the grammarian in me would also insist that there be a hyphen in the name, so gluten free Black-Bottom Cupcakes, but again, who really cares except me?

gluten free black bottom cupcakes | gfJules

And who would honestly want something called a “Brown-Bottom Cupcake”? Ok, I digress.

Allow me one more digression: is it weird that I can’t even say the words gluten free Black Bottom Cupcakes without thinking of the Queen song “Fat Bottomed Girls”? Embarrassing, maybe, but regardless of the words, the song is hopelessly catchy. But no hyphen. I checked.

gluten free black bottom cupcake with bite

Regardless of whether you care to use a hyphen or not, you need to try these moist and delicious mini gluten free cakes of chocolate-cream-cheese deliciousness. They’ll make your rockin’ world go ’round.

P.S. Check out my Facebook Live video showing every step of how easy it is to make these delightful cupcakes (click on the photo below to watch on YouTube)!

Jules shows how to make gluten free black bottom cupcakes
Click on the photo to watch how to make these yummy gluten free black bottom cupcakes!

Note that in my recipe I made these entirely dairy-free with some great ingredient substitutions, so don’t shy away from this recipe just because of the “cream cheese” topper. 

Here’s what these cute little cupcakes look like before baking — all made with dairy-free and gluten-free ingredients.

blackbottom cupcakes before baking

P.P.S. If you want to add some protein to your cupcakes — hey, why not? — I tried this recipe with OWYN protein powder. See the recipe notes below, but adding their vegan, gluten-free protein powder and/or drinks to this recipe can add up to 21 grams of protein to your yummy dessert. Now that’s something to get really excited about!**

gluten free black bottom cupcakes tall

If you try this recipe, I’d love to hear about it in the comments, and please leave a 5-star review if you love it!

Gluten Free Black Bottom Cupcakes

gluten free black bottom cupcakes

Black Bottom Cupcakes

Yield: 18 cupcakes
Prep Time: 20 minutes
Cook Time: 30 minutes
Total Time: 50 minutes

A classic dessert turned gluten free, dairy free and even vegan and high in protein if you choose. How sweet is that?


  • 8 ounces cream cheese, dairy or non-dairy (like Kite Hill Vegan Cream Cheese)
  • 1 egg or egg substitute (e.g. 1/4 cup firm silken tofu, blended with 1/2 tsp. baking powder)
  • 1/3 cup granulated cane sugar
  • 1/8 tsp. salt
  • 1/2 cup chocolate chips (Enjoy Life® Mini Chips)
  • 1 1/2 cups (203 gr) gfJules® All Purpose Flour
  • 1/4 cup (40 grams) GF vanilla pudding mix) or vanilla protein powder 1/4 cup=~25 grams)
  • 1/4 cup (20 grams) unsweetened cocoa powder
  • 1 tsp. baking powder
  • 1 tsp. baking soda
  • 1/4 tsp. salt
  • 3/4 cup brown sugar or coconut palm sugar
  • 1/3 cup vegetable or other mild cooking oil
  • 1/2 cup milk, dairy or non-dairy (like So Delicious® Coconut Milk Beverage) OR OWYN Vanilla Protein Drink*
  • 1/2 cup water
  • 1 Tbs. apple cider vinegar
  • 1 tsp. pure vanilla extract


Preheat oven to 350° F (static) or 325° F (convection).

Line 18 muffin tins with cupcake papers or lightly coat with oil.

Beat cream cheese, egg (or egg substitute), sugar and salt in a medium-sized bowl until lighter and well-mixed. Stir in the chocolate chips, cover and refrigerate until finished mixing the cupcake batter.

Whisk together the gfJules All Purpose Gluten Free Flour, dry pudding mix, cocoa, baking powder, baking soda and salt in a bowl and set aside.

In a large mixing bowl, mix brown sugar and oil until integrated. Add dry ingredient mix and slowly pour in the milk, water, cider vinegar and vanilla, beating until totally smooth.

Spoon the chocolate batter into each muffin cup, filling only 1/3 full. Top with a spoonful of cold cream cheese mixture in the middle — it does not have to cover the top of the muffin cup completely, or cover each cup evenly.

Bake for 30-35 minutes, or until a toothpick inserted into the cupcakes comes out with only dry crumbs and the cream cheese topping is beginning to lightly brown. Remove to cool on a wire rack.


* If you use OWYN Protein Powder in place of milk powder, you'll be adding 14 grams of protein to this recipe. If you also use OWYN Vanilla Protein Drink in place of milk, you'll be adding 7 more grams of protein to this recipe.

Did you make this recipe?

Please leave a comment (and maybe even a picture!) below or share a photo on Instagram! Be sure to tag me! @gfJules

I hope you love these cupcakes as much as we do!

Pin this recipe for later!

gluten free black bottom cupcakes | gfJules

Gluten Free Black Bottom Cupcakes are so moist, rich and full of flavor, you'll never miss the gluten or the dairy!

Gluten Free Black Bottom Cupcakes are so moist, rich and full of flavor, you'll n ever miss the gluten or the dairy! | gfJules

**I’ve partnered with OWYN (Only What You Need) to use their products in order to increase the nutrition in many popular gluten-free recipes. As always, all opinions are my own. See my disclosure policy for more information. Working with select brands I love allows me to keep bringing you free recipes, and I hope that in the process, you’ll learn about some of the safe gluten free products I choose for my family. Thanks so much for your support!



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    • Hi Angela, I can’t remember for sure, as I gather things like that throughout the years and then use them when it suits, but I likely found them at either Michael’s craft store or Marshall’s/TJ Maxx. I hope that helps!

  1. Hello,

    I tried a recipe printed in the Seattle Times for these cupcakes (they were called dessert muffins and weren’t gluten free). So I substituted. The amounts of ingredients in the recipe were almost identical except you have added milk powder (I can’t have milk or soy), cut the sugar, added baking powder and substituted milk for half the water called for. I also used Pamela’s All-Purpose Artisan Blend Gluten-free flour, and I substituted almond milk for the 1 cup of water called for.

    What I am mainly concerned about is the cream cheese mix you list is identical to the recipe in the paper. The Violife brand cream cheese substitute I used, combined with one egg, salt and sugar became very liquid upon mixing. In the oven it just ran all over the top of the muffins and didn’t come out with good texture or taste. For the second batch I added some tapioca flour to the cream cheese and it might have helped. I love the idea for these cupcakes, and want to make them taste good and have a good texture. But I am afraid to waste more good ingredients in another failure.

    Do you think that Kite Hill brand cream cheese substitute would work better than Violife brand? And I would have to use coconut milk powder (no protein in it) and almond milk instead of cow’s milk. Do you also think that using Jule’s all purpose gluten free flour mix would work better than the Pamela’s blend? (The chocolate portion of my cupcakes was a little tough.) Do you have any suggestions for me?

    • Wow, that’s a lot of changes and substitutions for me to comment on 🙂
      Taking things one at a time, having not seen the recipe you tried, but because you made a bunch of tweaks to it anyway, I guess I would say that since you did compare the recipes and they were quite similar, and you are asking if they might turn out better with my gfJules Flour anyway … I would start with suggesting that you try my recipe as written (I did create it to be dairy-free and soy-free, so you’re good there!) and use my gfJules Flour and see if that doesn’t solve the toughness problem and answer most of the questions in one fell swoop without you having to re-invent the recipe wheel, so to speak? My gfJules Flour will be noticeably lighter and softer than other blends like Pamela’s, so you should find it doesn’t make tough cakes.
      Regarding the Violife v. Kite Hill cream cheese filling — check out my review of dairy free ingredients here. I have noticed a wide variation in their melting properties. I have only used Violife in a few things, honestly, and if you had it turn super liquid-y, I would steer clear of it in the future for applications like this. Melt vegan butter is the same thing — a total disaster for making frostings, for example.
      Regarding the milk powder, you’re right that coconut milk powder doesn’t tend to have protein, but I’ve found that using brands that have some fiber and maltodextrin in them do lend some structure to the baked goods you’re adding them to. Something to try.
      Anyway, I hope these suggestions help – let me know how the experimenting goes!

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