Chocolate Cheesecake Cupcakes

These are also known as Black-Bottom Cupcakes, from David Liebovitz's "The Great Book of Chocolate." Smitten Kitchen and Annie's Eats have also posted this recipe with nice photos. See my notes at the bottom regarding the debate between regular-size muffins and mini-muffins, paper cups versus no paper cups, and filling to the brim versus filling to 90%.

Yield: 12 full-size or approximately 48 mini cupcakes

For the filling:
8 ounces cream cheese, regular or reduced fat, at room temperature
1/3 cup granulated sugar
1 large egg, at room temperature
2 ounces bittersweet or semisweet chocolate, coarsely chopped

For the cupcakes:
1 1/2 cups all-purpose flour
1 cup firmly packed light brown sugar
5 tablespoons natural unsweetened cocoa powder (not Dutch-process)
1 teaspoon baking soda
1/4 teaspoon salt
1 cup water
1/3 cup unflavored vegetable oil
1 tablespoon white or cider vinegar
1 teaspoon vanilla extract

Make the filling: Beat together the cream cheese, granulated sugar, and egg until smooth. Stir in the chopped chocolate pieces. Set aside.

Make the cupcakes:
1. Adjust the rack to the center of the oven and preheat to 350°F (175°C). Butter muffin tin, or line the tin with paper muffin cups. (See notes at bottom)
2. In a medium bowl sift together the flour, brown sugar, cocoa powder, baking soda, and salt. In a separate bowl, mix together the water, oil, vinegar, and vanilla.
3. Make a well in the center of the dry ingredients and stir in the wet ingredients, stirring until just smooth. Stir any longer and you will over mix the batter and end up with less-than-tender cupcakes.
4. Divide the batter among the muffin cups. Spoon a few tablespoons* of the filling into the center of each cupcake, dividing the filling evenly. This will fill the cups almost completely,** which is fine.
5. Bake for 25 minutes, or until the tops are slightly golden brown and the cupcakes feel springy when gently pressed. These moist treats will keep well unrefrigerated for 2 to 3 days if stored in an airtight container.

Notes:
* I made these into mini-muffins. It was just the right amount of batter for 2 full trays, or 48 mini-muffins. On the first batch, I used paper muffin cups and cooked them for about 17 minutes. This was too long, as the muffins were a bit dry and totally stuck to the muffin cups. Since they're so small anyway, when half of the muffin gets stuck to the paper, it's just not worth even trying. On the second batch, I sprayed the muffin tin and did not use muffin cups. I took them out after approximately 14 minutes and they were perfect. I used a toothpick to pop them out of the cups, and they were moist and delicious, with no paper to fiddle with. If I make these again, I will definitely skip the papers and use the shorter cook time.

* The recipe says for full-size muffins you can fill the cups to the brim with batter. I would not recommend this for the mini muffins. See Smitten Kitchen's post where she talks about her mini-muffins spilling over. She recommends filling the mini cups with 1 Tbsp of batter. This is exactly what I did and it was the perfect amount. I used a 1 Tbsp measuring spoon to dole out the chocolate batter, and a 1/2 tsp spoon for the cheesecake filling.