Boston cream pie cupcakes are homemade yellow cupcakes filled with pastry cream and topped with an easy chocolate ganache.

Boston cream pie cupcake on a piece of white parchment paper.

Boston cream pie cupcakes are delicious! I mean, what’s not to love?

Boston cream pie isn’t really pie. It’s actually made of sweet yellow cake, vanilla pastry cream, and rich chocolate ganache.

And it’s hard to go wrong with a combo like that! This recipe will leave you with several extra egg whites. Making homemade angel food cake is a great way to use up those extra egg whites.

Ingredients for Boston cream pie cupcakes in dishes.

How to make Boston cream pie cupcakes

Some Boston cream pie cupcake recipes use vanilla pudding for the filling and a yellow cake mix for the cupcakes.

This recipe takes a little more time because there are three homemade components: the cupcakes, the pastry cream, and the chocolate ganache.

MAKING THE PASTRY CREAM

Heat milk until hot and bubbly at the edges but not boiling.

While the milk it heating, whisk together sugar, flour, and salt in a small bowl.

In a medium bowl, whisk together egg yolks.

Flour and egg yolk mixture in a mixing bowl.

Gradually add the flour mixture to the egg yolks, whisking until incorporated before the next addition.

Stream milk into egg yolk mixture, whisking as you go (otherwise you will end up with scrambled eggs if you add it too quickly or all at once).

Once all of the milk is incorporated, return mixture to saucepan.

Cook, whisking continually, until it bubbles when you stop whisking it, about 4-5 minutes.

Remove from heat, and stir in vanilla extract.

Place pastry cream in a dish, and cover with plastic wrap. Press plastic wrap to the pastry cream (otherwise you’ll get a pudding skin on it).

Refrigerate at least 2 hours.

MAKING THE CUPCAKES

Preheat oven to 350 F. Generously grease and flour a 12-cup muffin tin (pan release works well) or use a cooking spray like Baker’s Joy that is a combo nonstick spray and flour.

In a medium bowl, whisk together flour, baking powder, and salt.

In the bowl of a stand mixer fitted with a paddle attachment, beat together butter, sour cream, and sugar until well-combined.

Add the eggs one at a time, beating well after each addition. Scrape down the bowl as needed.

Beat in milk and vanilla until well-combined.

Add flour mixture, and stir until just incorporated.

Divide batter between prepared muffin tins.

Bake 15-20 minutes, or until the cupcakes spring back when lightly pressed.

Cool cupcakes in the pan about 5 minutes, and then remove to wire rack to cool completely.

Once you’re ready to assemble the cupcakes, make the chocolate ganache.

MAKING THE CHOCOLATE GANACHE

Hot cream pouring onto chopped chocolate.

Place the chocolate chips in a heat-proof bowl.

Heat the cream over low heat until just simmering. Do not boil. Remove cream from heat and pour over chocolate chips.

Place a piece of aluminum foil over the bowl and seal. Let the cream/chocolate chips sit for 5 minutes without stirring.

Remove the foil. Stir until the chocolate chips have melted and mixture is smooth and well-combined.

Let the ganache sit, uncovered, for 30 minutes, stirring occasionally, to set up before using.

TO ASSEMBLE

Partially filled Boston cream pie cupcakes.

Cut top off of cupcake (the domed muffin top).

Using a small (1 tablespoon) cookie scoop, scoop out a piece of cake. Discard, eat, or otherwise use the cake.

Using the cookie scoop, scoop out a scoop of pastry cream, and place it in the scooped out portion of the cupcake.

Filled Boston cream pie cupcake without ganache on it.

Replace top of the cupcake, gently pressing the top onto the cream.

Top cupcake with some chocolate ganache.

Boston cream pie next to a dish of pastry cream.

Storing

The cupcakes should be stored in an airtight container in the fridge. The cupcakes will keep for up to 4 days when properly stored.

I don’t recommend freezing the assembled cupcakes. If you would like to make the cupcake portion ahead of time and freeze them, you can. However, I recommend making the filling and ganache just before serving.

Close up photo of a Boston cream pie cupcake.

More cupcake recipes!

If you’ve tried this Boston Cream Pie Cupcake recipe, don’t forget to rate the recipe and leave me a comment below. I love to hear from people who’ve made my recipes!

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