Step 1

Position a rack in the middle of the oven and preheat to 400 degrees. Line a regular size muffin pan with cupcake liners, tulip baking cups or homemade parchment liners (see Notes).

Step 2

In a small (2-quart) saucepan over medium heat, combine the milk, water, and instant coffee or espresso powder, and bring to a simmer, whisking occasionally. Add the cocoa powder and whisk until fully incorporated. Decrease the heat to low, add 1/2 cup (85 grams) of the chocolate chunks and the butter, and whisk until melted and smooth, about 1 minute. Remove from the heat and transfer the mixture to a large bowl to cool slightly.

Step 3

In a medium bowl, whisk together the flour, baking powder and salt until well combined.

Step 4

To the bowl with the chocolate mixture, add the brown sugar, granulated sugar, oil, eggs and vanilla, and whisk until thoroughly combined. Add about one-third of the flour mixture and whisk until incorporated. Add the remaining flour mixture and, using a flexible spatula, gently fold until almost no dry streaks remain. Then, gently fold in the remaining 1/3 cup (60 grams) of chocolate chunks and the chopped milk chocolate (or milk chocolate chips), until just combined. Do not overmix.

Step 5

Using a No. 16 disher or 1/4-cup (60-milliliter) measuring cup, evenly divide the batter among the muffin cups, filling each cup to the top of the muffin pan (or a little higher if using tulip baking cups or homemade liners). Sprinkle additional chocolate chunks and chopped milk chocolate (or milk chocolate chips) on top. Transfer the pan to the oven and immediately reduce the oven temperature to 375 degrees. Bake for 22 to 24 minutes, or until a toothpick inserted in the center of a muffin comes out clean. (You don’t want any batter clinging, but you may hit pockets of melted chocolate with the toothpick.)

Step 6

Let the muffins cool in the pan for 10 minutes, then use a butter knife or the wide end of a piping tip to cut or punch out an approximately 3/4-inch-wide hole in the center of each muffin. (Snack on the centers or save them to use as an ice cream topping.) Let the muffins cool completely, about 30 minutes.

Step 7

Make the ganache: While the muffins are baking, in a small (2-quart) saucepan over medium-low heat, combine the chocolate chunks, heavy cream and salt, and cook, stirring frequently, until melted and smooth. Remove from the heat and let cool completely, 30 to 40 minutes.

Step 8

Once the muffins and ganache are completely cool, spoon or pipe the ganache into the center of each muffin, filling up the hole just until it starts to overflow. (Leftover ganache can be used as a filling or topping for other desserts, or chilled and rolled into truffles.) Serve immediately.