Preheat oven to 350. Line a 12-cup muffin tin with paper liners.
In a large bowl, whisk together the flours, sugar, baking powder, and salt. Add the beaten eggs, melted butter, milk, and stir well with a wooden spoon or rubber spatula to combine.
Divide the batter evenly among the muffin cups. Bake until a toothpick inserted in the center comes out clean, 20 to 25 minutes.
As soon as the cupcakes come out of the oven, press down on the center of each with the back of a tablespoon, to create a shallow indentation. Fill each indentation with about 2 teaspoons of jam, then transfer the cupcakes to a cooling rack to cool completely. Once cool, dust the edges with confectioner’s sugar.
