Preheat oven to 350 degrees Fahrenheit (175 degrees Celsius) and line a 12-cup muffin tin with paper liners.
In a large bowl, whisk together the whole wheat flour, cocoa powder, baking soda, and salt.
In a separate medium bowl, whisk the Greek yogurt, maple syrup, egg, vanilla extract, and almond milk until smooth.
Pour the wet ingredients into the dry ingredients and stir until just combined; do not overmix.
Fold in 0.25 cup of the dark chocolate chips.
Divide the batter evenly among the muffin cups and sprinkle the remaining chocolate chips on top.
Bake for 18 to 22 minutes, or until a toothpick inserted into the center comes out clean.
Allow muffins to cool in the tin for 5 minutes before transferring to a wire rack.