Start by preheating your oven to 350 degrees Fahrenheit. While it heats up, line your muffin tin with paper liners or lightly grease each cup with cooking spray so nothing sticks later.
In a medium bowl, whisk together the flour, baking soda, cinnamon, and salt until fully combined. This step spreads the leavening evenly through the flour so your muffins rise consistently in the oven.
In a large bowl, whisk the eggs, olive oil, honey, and brown sugar together until smooth. Then stir in the grated apple with its juices, along with the grated carrots and zucchini.
Add the dry ingredients into the wet mixture and use a spatula to fold them together until just combined. Gently stir in the raisins and shredded coconut without overmixing the batter.
Divide the batter evenly among your muffin cups, filling each about three-quarters full. Bake for 20 to 22 minutes, or until a toothpick inserted in the center comes out clean.
Let the muffins cool in the tin for about five minutes before transferring them to a wire rack. Once fully cooled, they're ready to pack straight into a lunchbox or store for later.