1. Prepare Your Oven and Muffin Tin: Start by preheating your oven to 375 F (190 C). Line a 12-cup muffin tin with paper liners or grease it thoroughly with cooking spray. This prevents sticking and makes for easy cleanup.

2. Combine Dry Ingredients: In a large mixing bowl, whisk together the whole wheat flour, baking powder, baking soda, salt, and black pepper. Make sure there are no lumps and the ingredients are evenly distributed.

3. Add Your Veggies and Cheese: To the dry ingredients, add the squeezed dry grated zucchini, grated carrots, finely chopped onion, and shredded cheddar cheese. Stir gently until the vegetables and cheese are well coated with the flour mixture. This step helps prevent the vegetables from sinking to the bottom of the muffins.

4. Mix Wet Ingredients Separately: In a separate medium bowl, lightly beat the eggs. Then, whisk in the milk and olive oil (or melted butter) until thoroughly combined.

5. Combine Wet and Dry Mixtures: Pour the wet ingredient mixture into the bowl with the dry ingredients and vegetables. Stir gently with a spoon or spatula until just combined. Be careful not to overmix; a few lumps are perfectly fine and will lead to tender muffins. Overmixing can result in tough muffins.

6. Fill Muffin Cups: Divide the batter evenly among the 12 prepared muffin cups. You can use a large spoon or an ice cream scoop for this. Fill each cup about two-thirds full.

7. Bake Until Golden: Place the muffin tin in the preheated oven and bake for 20-25 minutes, or until the tops are golden brown and a wooden skewer or toothpick inserted into the center of a muffin comes out clean.

8. Cool and Serve: Once baked, remove the muffin tin from the oven and let the muffins cool in the tin for 5 minutes before transferring them to a wire rack to cool completely. Serve warm or at room temperature.