Sift the whole wheat flour, cocoa powder, baking powder, baking soda, and salt into a large bowl to ensure everything blends smoothly without any lumps.
In a separate bowl, whisk the melted coconut oil, honey (or maple syrup), eggs, and vanilla extract until the mixture is smooth and creamy for added moisture.
Pour the wet ingredients into the dry mix and gently stir with a spatula. Be careful not to overmix, it's okay if the batter has a few lumps.
Slowly add almond milk to loosen the batter, folding it until it reaches the right consistency, thick but scoopable.
Fold in the chocolate chips (or your preferred mix-ins) until they’re evenly spread throughout the batter.
Spoon the batter into a muffin tin, filling each cup. Use muffin liners or lightly grease the tin for easy removal.
Bake at 350°F for 18 minutes. Test if they’re done by pressing lightly on the tops or using a toothpick, it should come out clean.
Let the muffins cool in the tin for a few minutes before transferring them to a wire rack to finish cooling. Then, enjoy your fresh, healthy chocolate muffins!