Preheat oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners or coat with non-stick spray.
In a medium mixing bowl, whisk together the whole wheat flour, baking powder, baking soda, and sea salt until well combined.
In a separate large bowl, whisk the Greek yogurt, maple syrup, eggs, melted coconut oil, and vanilla extract until the mixture is smooth.
Pour the dry ingredients into the wet ingredients and fold gently with a spatula until just incorporated, ensuring the batter is not overmixed.
Gently fold the dark chocolate chips into the batter.
Distribute the batter evenly into the prepared muffin tin, filling each cup approximately three-quarters full.
Bake for 18 to 22 minutes or until a toothpick inserted into the center of a muffin comes out clean.
Remove from the oven and allow the muffins to cool in the pan for 5 minutes before transferring to a wire rack to cool completely.