Preheat oven to 180ºC (356ºF). Line a 12-hole regular sized muffin pan with muffin liners. Set aside.
In a small mixing bowl, combine flour, cocoa powder, baking powder and baking soda, mix well and set aside.
In a large mixing bowl, add butter. Take a hand mixer or a stand mixer fitted with the paddle attachment, lightly beat the butter for a few seconds just to break it down. Add coconut sugar and beat on high for 1 minute until well combined and fluffy.
Add eggs, yoghurt and vanilla. Beat on medium speed for 30 seconds or until light and well combined, scraping down the sides when needed.
Add dry flour mixture into creamed mixture. Beat until just combined.
Pour in milk, beat until milk has combined and mixture forms a soft batter, ensuring not to over-mix.
Gently fold through first measurement of chopped chocolate.
Spoon batter evenly amongst liners, filling each one just below the top edge.
Sprinkle each muffin with second measurement of chopped chocolate.
Bake for 15-20 minutes or until a skewer inserted into the middle comes out clean.
Cool in pan for 5 minutes.
Remove and transfer to a wire rack to cool completely.
Store in an airtight container, in the pantry, for 4-5 days.