Vegan Black Bottom Cupcakes

Black Bottom Cupcakes from Vegan Chocolate by Fran Costigan. Photo ©Kate Lewis
Black Bottom Cupcakes from Vegan Chocolate by Fran Costigan. Photo © Kate Lewis
Photo from Vegan Chocolate by ©Kate Lewis

I loved cream cheese and bagels growing up on Long Island. Sure there was lox, but what I loved was the cream cheese. As a vegan, I hadn’t eaten any authentic tasting cream cheese in so many years, but now we have some very good dairy-free cream cheeses available to us. Because I got to test the new plain cream cheese from Miyokos Kitchen, I decided to make a batch of Black Bottom Cupcakes this week.

Here’s the thing—when I was trying to replicate black bottom cupcakes, a recipe, that I had to have for my cookbook Vegan Chocolate, I was not using egg replacer and it was, unbelievably, in pre-aquafaba days. I still stand by the chia gel that replaces the egg in the book’s recipe, but with a few tubs of cream cheese in my refrigerator, I decided to test 3 different versions.  I will be discussing Best Practices for Recipe Testing at my September 27th Live Event for Rouxbe, and you are all welcome to join in. The event is free, at 1:00pm Pacific time. Just register here:

When I test recipes, I cut them in half. Here, I made the cream cheese mixture, to the point of adding the egg replacers, divided it in half, noting both cup and volume measures. Then I added 1/2 of 2 of the 3 egg replacers to each half. Then, I labeled and refrigerated the mixtures while I made the batter.

The three egg replacers tested were:

  1. Chia gel per the published recipe.
  2. Egg replacer. I used Bob’s Red Mill.
  3. 3 tablespoons aquafaba with a pinch of cream of tartar mixed in.
Chia Seeds
Chia seeds

My conclusions: All tasted good to me, and my tasters agreed. The 3 ‘eggs’ behaved differently.

  1. The chia gel:  The recipe has held up and I will be sticking with it as first choice.
  2. The egg replacer worked well, and gave a similar but different result, almost a self frosted cupcake. I will use it if I am out of chia seeds or don’t want to grind them.
  3. The aquafaba baked up into a self frosted cupcake, which is not a bad thing, at all, but different.


Black Bottom Cupcakes recipe testing

The amounts of filling with the different egg replacers differed. When testing, I divide the filling as evenly as possible. With these cupcakes, some always have more than others, which was not a problem. It’s important to note that standard size cupcake pans have different capacities. Measure the volume and keep the notes.

I suggest you start with the following easy vegan version of the beloved retro recipe for Black Bottom Cupcakes from Vegan Chocolate. It is irresistible! I am bringing a pan of these cupcakes to my daughter’s home tonight for Rosh Hashanah dinner. For those who celebrate, L’Shana Tova.

Black Bottom Cupcakes from Vegan Chocolate by Fran Costigan. Photo ©Kate Lewis
Photo ©Kate Lewis
Black Bottom Cupcakes from Vegan Chocolate by Fran Costigan. Photo ©Kate Lewis

Black Bottom Cupcakes

Fran’s Rules: Before you begin, read the recipe all the way through. Position the oven rack, and preheat the oven. Prepare your mise en place, both equipment and ingredients. This sounds like a lot of work? Nope, it’s fast and organized and makes baking and eating a pleasure. Adjust the amount of filling for smaller cupcakes.
Servings 12 standard-size cupcakes or 24 minis



  • 1 1/2 teaspoons / 3 grams ground chia seeds
  • 1 1/2 tablespoons / 22.5 ml water
  • 8 ounces / 227 grams nondairy cream cheese spread, straight from the refrigerator
  • 9 tablespoons / 56 grams organic confectioners’ sugar, sifted
  • 2 teaspoons / 10 ml pure vanilla extract
  • 2 ounces / 85 grams chocolate chips or chopped chocolate


  • 1 cup / 129 grams organic all-purpose flour
  • 1/2 cup / 70 grams organic whole wheat pastry flour
  • 3/4 cup / 159 grams organic granulated sugar
  • 1/4 cup / 50 grams organic whole cane sugar, ground in a blender until powdered
  • 1/4 cup plus 1 tablespoon / 25 grams natural cocoa powder. non-alkalized
  • 1 teaspoon / 5 grams baking soda
  • 1/4 teaspoon fine sea salt
  • 1 cup / 240 ml any nondairy milk
  • 6 tablespoons / 90 ml mild tasting extra-virgin olive oil or organic neutral vegetable oil
  • 1 tablespoon / 15 ml apple cider vinegar
  • 1 teaspoon / 5 ml pure vanilla extract
  • 1 teaspoon / 5 ml chocolate extract optional



  • Mix the chia and water and set aside for a couple of minutes. Mix with a fork until thoroughly combined. Repeat twice, 5 minutes apart. The chia gel can be made a day ahead and refrigerated in a covered container. Mix before using.
  • Beat together the cream cheese, sugar, and vanilla with an electric mixer. Add the chia gel and mix on medium for another 30 seconds until incorporated. Stir the chocolate chips into the filling. Refrigerate in a covered container while you make the cupcakes.

Make The Cupcakes

  • Position a rack on the rung just above the center of the oven and preheat to 350°F / 180°C. Lightly oil the top only of a 12-cup cupcake tin to make any bake-overs easier to clean, and line with paper liners that are slightly higher than the cups.
  • Put a wire mesh strainer over a medium bowl. Add the all-purpose flour, pastry flour, granulated sugar, whole cane sugar, cocoa, baking soda, and salt to the strainer. Stir with whisk to sift the ingredients into the bowl and whisk to aerate. (If any very small bits remain in the strainer, add them to the mixture in the bowl.) Whisk to aerate the mixture.
  • In a separate small bowl, mix the nondairy milk, oil, vinegar, vanilla, and chocolate extract (if using) until thoroughly mixed. Immediately pour into the dry ingredients. Whisk hard until the batter is smooth.
  • Fill the cups close to three-quarters full with batter. Spoon or scoop about 3 tablespoons of the filling—but not more—into the center of each cake. The cups will be filled almost to the top. That’s okay. You may not have even amounts of the batter—this is not a recipe for those of us with OCD tendencies.
  • Bake for 25 to 27 minutes, or until the edges of the cakes are firm when lightly tapped and the filling is set. Set the tins on a wire rack for 10 minutes. The filling will collapse into the cakes while they cool. Remove the cupcakes from the tin, and cool completely on a wire rack before serving.
  • Serving: I like to serve the cupcakes slightly chilled for the best flavor, but some of my testers liked the cakes best at room temperature. You’ll just have to make two batches and try them each way to decide!
  • Keeping: Refrigerate in an airtight container for up to three day.
  • They can be frozen and defrosted.


You may not have even amounts of the filling—this is not a recipe for those of us with OCD tendencies. Do not substitute alkalized (Dutch-process Cocoa). If you cannot find natural cocoa, and like me will not use Hershey’s, use a raw cocoa. It is non-alkalized.
From Vegan Chocolate: Unapologetically Luscious and Decadent Dairy-Free Desserts, © 2013 by Fran Costigan, Running Press. Photo credit: Kate Lewis
Tried this recipe?Let us know how it was!



  • 5 stars
    I have made the Black Bottomed Cupcakes a number of times since buying the cookbook. I would say 6-7 times.
    I use a cashew cream as the cheese..but I am afraid I have been making it too watery. The mixture never penetrates the cupcake but becomes a layer on top. But, my go to cup cake is the Chocolate Date…people go nuts on those!

    • Hi Donn
      The cashew cream is not a good replacement for the cream cheese and flax egg
      , as you learned. But I’m curious about the looks and flavor of the layer on top. It sounds as if you invented a self frosting cupcake.

      I’m glad TIU like the Chocolate Date Cake.

      Thanks for writing.


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