Mini Gluten-Free Boston Cream Pies | Mary Fran, Cupcake Therapist

You'll be yelling WHOOPIE! when you taste these mini Boston Cream Whoopie Pies.

These Mini Gluten-Free Boston Cream Pies are adorable and oh-so delicious. Like seriously. The only caveat is that they don’t travel well, so if you’re bringing them to a party, assemble them once you arrive.

Courtesy:  Mary Fran Wiley, Frannycakes

I really think that my coworkers are trying to stump me when it comes to making them birthday treats. Pulling whatever kind of flavor they can out of their heads to see if I really can do it. I mean, we had gluten-free peanut butter & jelly cupcakes and gluten-free double chocolate peanut butter cupcakes this summer.


This time the request was for Boston Cream Pie Cupcakes – something that was actually a bit more traditional and a little less out there.

I decided that I was bored with the core & fill kind of cupcake, so I went a different route with these – I used a mini whoopie pie pan to make the cake pieces and then piped in some filling and poured on a thick glaze. And ended up with two-bite treats that were all gone before lunch.


The only caveat is that these do not transport well. If you try to take them on your 2-train 2-hour commute, they might just get a little banged up before you get them in to the office. (It won’t effect the flavor, but it might bruise your ego a wee bit). If these need to make a trip, I would bring all the components and assemble on-site. It takes about 10 minutes to combine all the parts into lovely little mini gluten-free boston cream (whoopie) pies.

Mini Gluten-Free Boston Cream Pies

Mini Gluten-Free Boston Cream Pies - two-bite whoopie pies, filled and glazed, and guaranteed to be gone before lunch!

Course Dessert
Cuisine American
Keyword dessert, whoopie pie
Author Mary Fran Wiley


For the Cakes

  • 175 grams or 1¼ cups gluten-free cake flour (143g high-quality all-purpose gluten-free flour + 4 tablespoons (32g) cornstarch)*
  • ½ tsp xanthan gum omit if your blend already contains it
  • ½ tsp baking powder
  • ¼ tsp baking soda
  • ¼ tsp kosher salt
  • 109 grams, or 1/2 cup packed light brown sugar
  • 28 grams, or 2 TBSP unsalted butter, melted and cooled
  • 24 grams, or 2 TBSP vegetable shortening, melted and cooled
  • 1 extra-large egg at room temperature beaten
  • 1 tsp vanilla bean paste or replace with equal volume pure vanilla extract
  • ½ cup plus 2 TBSP buttermilk

For the pastry cream

  • 30 grams, or 1/4 cup cornstarch
  • 150 grams, or 3/4 cup divided
  • 2 cups milk I don’t drink milk, so I almost always use almond milk , divided
  • 4 egg yolks
  • 1 tsp vanilla bean paste
  • 2 TBSP butter
  • pinch of salt

Chocolate Glaze

  • 130 grams, 4.5 oz bittersweet chocolate, roughly chopped
  • 60 grams, or 4 TBSP butter
  • 1 TBSP corn syrup


  1. Preheat your oven to 325 degrees F and grease a mini whoopie pie pan.
  2. In a large bowl, place the flour, xanthan gum, baking powder, baking soda and salt and whisk to combine well.
  3. Whisk in the brown sugar, making sure you remove any lumps.
  4. Next, mix in the butter, shortening, egg and vanilla and make sure everything is well combined.
  5. Now, add the buttermilk, and mix again to combine well. You will have a batter that is somewhere between cake batter and cookie dough in consistency.

  6. Using a small scoop or you can pipe about as much as a large marble to each well of your whoopie pie pan.
  7. Bake on a center rack for 8-10 minutes, or until the cakes bounce back when pressed gently in the center. Remove from the oven and allow to cool in the pan for 10 minutes before transferring to a wire rack to cool completely. Repeat with the remaining batter.

Make the pastry cream

  1. Prepare an ice bath.
  2. In a small mixing bowl, combine ¼ cup sugar, egg yolks and the creamer (or ½ cup milk).
  3. In a medium sauce pan over medium heat, bring the remaining 1½ cups milk to a boil, stirring constantly.
  4. Remove from heat and add the hot milk to the egg mixture about a third at a time to temper the eggs. If you do this too fast you will end up with scrambled egg yolks and not a smooth cream.
  5. Return the pot to the stove and add the egg mixture. Over medium heat, keep whisking until the cream thickens and when you scrape the bottom of a pot, the cream does not close the gap immediately. Stir in the vanilla, salt and butter.
  6. Put the pot over your ice bath and stir every 5-10 mintues for about half an hour, or until the cream has cooled.

Make the glaze

  1. When you are ready to assemble the mini boston cream pies, melt together the chocolate, butter and corn syrup over low heat. If the mixture is not pourable, add an extra tablespoon of butter.

Assemble the cakes

  1. Pipe the pastry cream onto half of the cake pieces. Take one of the other cake pieces and top each one. Pour or spread chocolate glaze on each mini Boston cream pie.

Recipe Notes

*I use Cup4Cup Gluten-Free All-Purpose flour, and if you don’t have cornstarch, you can use it for the full amount called for here, the cakes will just be a little denser. This recipe will work with almost any GF AP Blend but it will not work with bean-flour based blends or baking mixes that contain baking powder or baking soda.