Preheat the oven to 180°C (350°F) and line a 12-cup muffin tin with paper liners.
In a large bowl, sift together the all-purpose flour, baking powder, baking soda, salt, and granulated sugar.
In a separate bowl, whisk the eggs, plain yogurt, vegetable oil, and vanilla extract until smooth and combined.
Pour the wet ingredients into the dry ingredients and gently fold together until just combined, being careful not to overmix.
Divide the batter evenly into two bowls.
Add the unsweetened cocoa powder and milk to one bowl and gently fold until the cocoa is fully incorporated.
Spoon a tablespoon of the vanilla batter into each muffin cup, followed by a tablespoon of the cocoa batter on top.
Use a skewer or knife to gently swirl the two batters together to create a marbled effect.
Bake in the preheated oven for 18-20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Remove the muffins from the oven and allow them to cool in the tin for 5 minutes before transferring to a wire rack to cool completely.