Preheat the Oven: Preheat your oven to 350°F (175°C). Line a muffin tin with paper liners or grease it lightly with coconut oil.
Mix Dry Ingredients: In a large mixing bowl, whisk together the whole wheat flour, almond flour, cocoa powder, baking powder, baking soda, and salt until well combined.
Prepare Wet Ingredients: In a separate bowl, beat the eggs and then add Greek yogurt, honey (or maple syrup), melted coconut oil, and vanilla extract. Mix until smooth. Slowly add the almond milk, mixing continuously to combine.
Combine Wet and Dry Ingredients: Gradually add the wet ingredients to the dry ingredients, mixing until just combined. Be careful not to overmix, as this can make the muffins dense.
Fold in Chocolate Chunks: Gently fold in the dark chocolate chunks, ensuring they are evenly distributed throughout the batter.
Fill Muffin Tin: Spoon the batter into the prepared muffin tin, filling each cup about 2/3 full. You can sprinkle a few extra chocolate chunks on top for a visually appealing finish.
Bake: Bake in the preheated oven for 18-22 minutes, or until a toothpick inserted into the center of a muffin comes out clean. Be careful not to overbake.
Cool and Enjoy: Allow the muffins to cool in the tin for about 5 minutes before transferring them to a wire rack to cool completely. Enjoy warm or at room temperature!