Boston Cream Pie Cupcakes {Grain-Free}

By Sara McGlothlin

I love Boston Cream Pie. I have this vivid memory from childhood of it being served for my dad’s birthday. Naturally, I then got this thought in my head that it was one of his favorite desserts (because aren’t birthdays all about enjoying your favorite dessert??). I’m still not sure it if is entirely true, but it is definitely one of my favorite desserts.

Healthifying the custard filling of the Boston Cream Pie was what tripped me up for years. My first attempt was during a time when I thought there needed to be a plant-based or more nutrient dense replacement for any traditional baking ingredient (i.e. butter, sugar, flour, oil). I have gradually chiseled away some wiggle room into my recipe writing to create more balance. Sometimes the real deal isn’t so bad after all when eaten in moderation.

That being said, I would still consider my recipe for custard an upgrade. In fact, when I was researching other Boston Cream Pie Cupcakes, many bloggers used Jello vanilla pudding from a box. While this is an option if you really want a short-cut (no judgement), I knew I could do better.

Coconut cream, egg yolks, gelatin, arrowroot starch, powdered monk fruit are all examples of healthier ingredients I incorporate into my custard. And yes, there is butter, but feel free to substitute with vegan butter if you wish. I love the end result and would even eat it with a spoon (may or may not already have!), but that is just me. It is so delicious in these cupcakes, and while this recipe might be a tad more elaborate than if you were to throw some batter into a muffin tin, it truly is a labor of love. When I made them, I was having a bit of an off day. The process put me in the flow, allowed me to work with my hands, there were delicious cupcakes on the other side, and I immediately felt better. That is the beautiful thing about baking.

I do recommend getting some round cookie cutters of various sizes to have on hand. They are great for creating the “filling” element in muffins and cupcakes. I have a set like this one.

Planning and prep

When I made this recipe, I baked the cupcakes the day before I made the custard and frosting, and I thought that worked well. This gives the cupcakes time to cool and chill in the refrigerator overnight. They become firmer and easier to work with the next day. Not only are you better able to “cookie cut” the center for the filling, but they are then ready to be be frosted. Otherwise, the cupcakes have to completely cool before taking those next steps, which at a minimum is two hours. The custard needs an hour to chill at room temperature as well before it thickens and reaches the right consistency. As I said in the Boston Cream Pie post, it remains thin and runny until about minute 0:45 – 0:50, and then thickens quickly. The hour mark is the perfect time to fill the cupcakes. If you don’t have a small cookie cutter like in the photo above, you can cut the cupcake in half horizontally and place a spoonful of the custard between the two pieces to reach a similar effect. You can also use a knife to slice a small hole in the center.

Boston Cream Pie in a cupcake. Moist cake filled with vanilla custard cream and topped with chocolate buttercream frosting. Grain-free
Course Dessert
Servings 12 servings


  • muffin tin
  • Hand beater or stand mixer
  • 1 inch biscuit/cookie cutter or knife


For the cupcakes

  • 1/2 cup almond milk or dairy-free milk of choice
  • 1 teaspoon apple cider vinegar
  • 2 cups almond flour
  • 3/4 cup coconut sugar
  • 1/4 cup coconut flour
  • 2 tablespoons tapioca starch
  • 1 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1/4 teaspoon sea salt
  • 2 eggs, beaten
  • 1/2 cup unsweetened applesauce
  • 1/4 cup maple syrup
  • 1 teaspoon vanilla extract

For the custard filling

  • 1 cup full-fat coconut cream
  • 1 tablespoon gelatin Like Vital Proteins brand
  • 3 egg yolks
  • cup powdered erythritol sweetener like powdered monk fruit, or use powdered sugar
  • 3 tablespoons unsalted grass-fed butter ghee, or vegan butter
  • 2 teaspoons vanilla extract
  • 1 teaspoon arrowroot starch

For the chocolate frosting

  • 1/2 cup coconut oil room temperature
  • 1/2 cup grass-fed butter or vegan butter room temperature
  • 1/3 cup raw cacao powder or unsweetened cocoa powder
  • 1 cup powdered monk fruit or substitute with regular powdered sugar


  • Make the cupcakes. Preheat the oven to 350°F. Line a muffin tin with cupcake liners.
  • In a medium bowl, whisk together the almond milk and apple cider vinegar.
  • In a separate large bowl or stand mixer, mix the almond flour, coconut sugar, coconut flour, tapioca starch, baking powder, baking soda, and salt. Stir to blend.
  • To the medium bowl with the milk and vinegar mixture, whisk in the eggs, applesauce, maple syrup, and vanilla extract until creamy.
  • Pour the wet ingredients into the bowl with the flour mixture and beat until a batter is formed. Let the batter rest in the bowl for 10 to 15 minutes.
  • Evenly distribute the batter between the cupcake liners, filling them about 3/4 of the way to the top. Bake for 22 to 25 minutes until a toothpick inserted into the center comes out clean. Allow the cupcakes to completely cool in the muffin tin before incorporating the custard and frosting.
  • Make the custard. In a small saucepan over medium heat, slightly warm the coconut cream, about 1 minute. Add the gelatin and whisk vigorously until dissolved. Bring to a simmer. If there are still clumps, that is OK, they should dissolve eventually.
  • Meanwhile, whisk together the egg yolks and powdered sugar. Once the coconut cream and gelatin mixture is simmering, add half to the yolk and sugar mixture and whisk to combine. Pour it back into the saucepan and whisk until everything is creamy. Continue to cook until slightly reduced, whisking constantly, about 4 minutes. Be sure to watch the saucepan, the mixture can heat quickly and the egg can curdle.
  • Remove from heat and whisk in the butter and vanilla extract. Add the arrowroot starch and whisk vigorously until dissolved. Alternatively, if there are still clumps, you can transfer the mixture to a blender and process until smooth. Transfer the mixture to a small glass or ceramic bowl. Allow to cool about 1 hour until thickened, stirring occasionally (**see note). Use immediately.
  • To make the frosting, combine the coconut oil and butter (or vegan butter) in a large bowl. Beat with a hand mixer or immersion blender with the whisk tool until fluffy, about 30 seconds.
  • Add the cacao powder or cocoa powder, and powdered monk fruit and beat again until everything is combined. Use a spatula to scrape down the sides as you need to.
  • Using a spatula, mix the frosting. Use immediately, or place in the refrigerator for 10 minutes for a denser texture.
  • To assemble the cupcakes: once the cupcakes have completely cooled, use a 1-inch biscuit/cookie cutter to cut a hole in the center. You can also use a knife to create a well. Reserve the top. Transfer about a tablespoon or so of the custard into the center of the cupcake, and place the top back on. Spoon frosting on top or use a piping bag to frost.
Keyword Gluten-free, Grain-free, Keto-friendly