Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners.
In a large bowl, sift together the all-purpose flour, cocoa powder, baking powder, baking soda, and salt. Stir in the granulated sugar.
In a separate medium bowl, whisk together the buttermilk, vegetable oil, eggs, and vanilla extract until well combined.
Pour the wet ingredients into the dry ingredients and gently fold together until just combined. Do not overmix.
Fold in the semi-sweet chocolate chips evenly through the batter.
In a small bowl, beat the softened cream cheese, granulated sugar, egg yolk, and vanilla extract until smooth and creamy to make the cream cheese filling.
Fill each muffin liner about halfway with chocolate batter.
Add one tablespoon of the cream cheese filling on top of the batter in each muffin cup.
Top each muffin with the remaining chocolate batter, covering the cream cheese filling completely.
Bake for 18 to 20 minutes, or until a toothpick inserted into the chocolate muffin portion (not the cream cheese center) comes out clean.
Remove the muffins from the oven and let them cool in the tin for 5 minutes, then transfer to a wire rack to cool completely.