Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners.
In a large bowl, whisk together the all-purpose flour, unsweetened cocoa powder, 1 cup granulated sugar, baking powder, baking soda, and salt.
In a separate medium bowl, whisk together the buttermilk, vegetable oil, 1 large egg, and 1 teaspoon vanilla extract until combined.
Pour the wet ingredients into the dry ingredients and stir gently until just combined. Do not overmix.
Fold in the semi-sweet chocolate chips.
In a small bowl, beat the softened cream cheese, 1/3 cup granulated sugar, 1 large egg, and 1/2 teaspoon vanilla extract until smooth and creamy.
Fill each muffin cup about halfway with the chocolate batter.
Add about 1 tablespoon of the cream cheese mixture on top of the chocolate batter in each cup.
Top each muffin cup with the remaining chocolate batter, covering the cream cheese filling.
Using a toothpick or skewer, gently swirl the cream cheese filling into the chocolate batter for a marbled effect.
Bake for 18 to 20 minutes, or until a toothpick inserted into the chocolate muffin part (not the cream cheese center) comes out clean.
Remove the muffins from the oven and let them cool in the tin for 5 minutes before transferring to a wire rack to cool completely.