Preheat oven to 350°F (175°C) and position the rack in the middle. Spread ½ cup (60g) all-purpose flour in a thin layer on a parchment-lined baking sheet and bake for 5 minutes, then remove and cool completely. Line a standard 12-count light-colored aluminum muffin tin with cupcake liners and set aside.

In the bowl of a stand mixer fitted with the paddle attachment, beat ½ cup (113g) softened unsalted butter and ¾ cup (150g) granulated sugar on medium speed for exactly 3 minutes until pale, fluffy, and nearly doubled in volume.

With the mixer on low, add 2 large room-temperature eggs one at a time, fully incorporating the first before adding the second. Add 2 tsp (10ml) pure vanilla extract, increase to medium speed, and beat for 30 seconds until smooth and cohesive.

In a separate bowl, whisk together 1½ cups (180g) all-purpose flour, 1½ tsp (6g) baking powder, and ¼ tsp (1.5g) fine sea salt. With the mixer on low, add the dry ingredients and ½ cup (120ml) whole milk in three alternating additions — dry, milk, dry, milk, dry — mixing only until each addition just disappears before adding the next. Stop as soon as the last streak of flour is gone.

Remove the bowl from the mixer. Toss ¾ cup (128g) semi-sweet chocolate chips in 1 teaspoon of flour, then fold into the batter with a silicone spatula using 10–12 slow strokes. Divide the batter evenly among the 12 lined cups, filling each to exactly two-thirds full (approximately 45–50g per cup).

Bake at 350°F (175°C) for 18–22 minutes until the tops spring back when lightly pressed and a toothpick inserted in the center comes out with a few moist crumbs. Leave in the tin for exactly 5 minutes, then transfer to a wire rack and cool completely — at least 1 hour — before frosting.

In a medium bowl, beat ¼ cup (57g) softened unsalted butter, ¼ cup (55g) packed light brown sugar, and 2 tbsp (25g) granulated sugar until smooth. Add 1 tbsp (15ml) whole milk, ½ tsp (2.5ml) vanilla extract, and 1 pinch fine sea salt and mix to combine. Add ½ cup (60g) cooled heat-treated flour and stir until a smooth dough forms. Fold in ¼ cup (43g) mini semi-sweet chocolate chips. Roll into 12 equal balls of approximately 18–20g each and refrigerate on a parchment-lined plate for 30 minutes.

In the cleaned stand mixer bowl, beat 1 cup (226g) softened unsalted butter on medium speed for 2 minutes until pale and creamy. Reduce to low and add 3 cups (360g) sifted powdered sugar in three additions. Add 1½ tsp (7.5ml) vanilla extract, 1 pinch fine sea salt, and 2 tbsp (30ml) heavy cream. Increase to medium-high and beat for 3 full minutes. Add the remaining 1 tbsp (15ml) heavy cream if needed to reach pipeable consistency.

Fit a large piping bag with a Wilton 1M open-star tip and fill two-thirds full with buttercream. Pipe a swirl onto each completely cooled cupcake starting from the outer edge and spiraling inward and upward in one continuous motion. Press one chilled cookie dough truffle into the center of each frosted cupcake, then scatter 3 tbsp (32g) mini semi-sweet chocolate chips evenly across all 12 cupcakes.