Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease the cups.
In a large bowl, sift together the all-purpose flour, unsweetened cocoa powder, baking powder, baking soda, and salt.
In a separate bowl, whisk together the granulated sugar, Greek yogurt, vegetable oil, eggs, vanilla extract, and milk until smooth and well combined.
Pour the wet ingredients into the dry ingredients and gently fold together using a spatula until just combined. Do not overmix; some lumps are okay.
Divide the batter evenly among the muffin cups, filling each about 3/4 full.
Bake in the preheated oven for 18 to 20 minutes, or until a toothpick inserted into the center of a muffin 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.