Preheat oven to 400°F. Line a 12-cup muffin tin with paper liners.
In a large bowl, whisk together the melted butter, sugar, eggs, Greek yogurt (or sour cream), milk, and vanilla until smooth.
In a separate bowl, whisk the fresh-milled flour, baking powder, baking soda, salt, and cocoa powder.
Add the dry ingredients to the wet ingredients and stir gently until just combined. Do not overmix.
Let the batter rest for 10–15 minutes to allow the fresh-milled flour to hydrate and soften.
Fold in the chocolate chips.
Divide the batter evenly among the 12 muffin cups. They will be full.
Bake for 15–18 minutes, or until a toothpick inserted in the center comes out clean or with moist crumbs.
Cool slightly before serving.