Preheat your oven to 350°F (175°C). This ensures your muffins bake evenly and rise beautifully.
Line a muffin tin with parchment liners or grease it lightly with cooking spray to prevent sticking.
Using a grater, shred the medium zucchini. You can leave the skin on for added nutrients. Set aside.
In a large mixing bowl, add the shredded zucchini, unsweetened applesauce, brown sugar, egg, Greek yogurt, and vanilla extract. Mix until well combined and smooth.
To the wet mixture, add the whole wheat flour, baking powder, baking soda, salt, and cinnamon. Stir gently until just combined. Be careful not to overmix.
Gently fold in the semi-sweet chocolate chips until evenly distributed throughout the batter.
Scoop the batter into the prepared muffin tin, filling each cup about 2/3 full to allow for rising.
Place the muffin tin in the preheated oven and bake for 18-20 minutes, or until a toothpick inserted into the center comes out clean.
Remove the muffins from the oven and let them cool in the tin for about 5 minutes before transferring them to a wire rack to cool completely.