Preheat your oven to 375 degrees Fahrenheit. Line a standard 12 cup muffin tin with tulip liners or paper liners and lightly spray with nonstick spray.
In a large bowl, whisk together the flour, baking powder, baking soda, and salt until evenly combined. Set aside.
In a medium bowl, whisk the melted butter with the granulated sugar and brown sugar for about 2 minutes until well combined and slightly glossy.
Microwave the Greek yogurt for 30 seconds and stir well. It should feel slightly warm, not hot. Add the warmed yogurt and the milk to the butter and sugar mixture. Whisk until fully combined with no streaks.
Add the eggs one at a time, whisking well after each addition.
Add the vanilla extract and whisk until smooth.
Pour the wet ingredients into the dry ingredients. Fold gently with a rubber spatula until just combined. Stop as soon as no dry flour streaks remain. Do not overmix.
Fold in the chocolate chips, reserving a small handful for topping.
Let the batter rest for 5 minutes. This allows the leavening to activate and helps the muffins dome evenly.
Scoop the batter into the prepared liners, filling each nearly to the top. Press a few reserved chocolate chips onto the top of each muffin.
Bake at 375 degrees Fahrenheit for 20 to 25 minutes, until the tops are set and golden. Do not rely on the toothpick alone. Press the top of a muffin gently with your finger. It should spring back completely with zero give. If it leaves any indent, bake for another 1 to 2 minutes.
Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.