Preheat your oven to 350°F (175°C) and line your muffin tin with parchment paper liners.
In a large mixing bowl, combine the all-purpose flour, baking powder, baking soda, salt, and orange zest (if using). Whisk together until well combined.
In another bowl, cream the unsalted butter and granulated sugar together until the mixture is light and fluffy. This should take about 3-4 minutes with an electric mixer.
Add the eggs, one at a time, mixing well after each addition. Then stir in the vanilla extract until combined.
Add the Greek yogurt to the wet mixture and stir until everything is well combined.
Gradually add the dry ingredients to the wet mixture, folding gently with a spatula until just combined. Do not overmix; a few lumps are okay!
Gently fold in the semi-sweet chocolate chips and chopped milk chocolate until evenly distributed throughout the batter.
Scoop the batter into the prepared muffin tin, filling each cup about three-quarters full.
Bake the muffins in the preheated oven for 18-20 minutes, or until a toothpick inserted in the center comes out clean.
Allow the muffins to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely. Enjoy your delicious Bakery Style Double Chocolate Muffins warm or at room temperature!