Preheat your oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease the cups with cooking spray.
In a large mixing bowl, whisk together the whole wheat flour, baking powder, baking soda, salt, and ground cinnamon until well combined.
In a separate bowl, whisk together the eggs, honey or maple syrup, unsweetened applesauce, almond milk, and vanilla extract until smooth.
Pour the wet ingredients into the bowl with the dry ingredients and mix until just combined.
Be careful not to overmix; it's okay if there are some lumps.
Fold in the grated carrots and zucchini until evenly distributed throughout the batter.
If using, gently fold in the chopped nuts and raisins or dried cranberries.
Divide the batter evenly among the prepared muffin cups, filling each cup about 3/4 full.
Place the muffin tin in the preheated oven and bake for 20-25 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Once baked, remove the muffins from the oven and let them cool in the muffin tin for a few minutes. Then, transfer the muffins to a wire rack to cool completely.
Serve the muffins warm or at room temperature. Enjoy them as part of your brunch spread or as a convenient grab-and-go breakfast option throughout the week.