Step 1: Prepare the Cream Cheese Filling

1. In a medium bowl, beat the softened cream cheese, powdered sugar, and vanilla extract together until smooth and creamy.
2. Transfer the cream cheese mixture into a piping bag or a zip-top bag with the corner snipped off. This will make it easier to fill the muffins later.
3. Place the filled piping bag in the refrigerator to firm up while you prepare the muffin batter.

Step 2: Prepare the Muffin Batter

1. Preheat your oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners or grease it with non-stick spray.
2. In a large bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, and nutmeg until well combined.
3. In a separate bowl, whisk the eggs, brown sugar, applesauce, honey or maple syrup, oil, and vanilla extract until smooth and fully incorporated.
4. Gradually add the wet ingredients to the dry ingredients, stirring just until combined. Do not overmix.
5. Fold in the shredded carrots and zucchini until evenly distributed throughout the batter. If you’re adding nuts or dried fruit, gently fold them in as well.

Step 3: Fill the Muffin Cups

1. Spoon about 2 tablespoons of the muffin batter into the bottom of each muffin cup, filling them about halfway.
2. Using the cream cheese piping bag, pipe about 1-2 teaspoons of the cream cheese filling into the center of each muffin cup. Be careful not to overfill, as the filling will spread while baking.
3. Cover the cream cheese filling with an additional tablespoon of muffin batter, ensuring the cream cheese is fully covered.
4. Fill each muffin cup until it is about ¾ full.

Step 4: Bake the Muffins

1. Place the muffin tin in the preheated oven and bake for 18-22 minutes, or until the muffins are golden brown on top and a toothpick inserted into the muffin (away from the cream cheese center) comes out clean.
2. Remove the muffins from the oven and allow them to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.

Step 5: Serve

1. Once the muffins have cooled, serve them at room temperature. Each muffin will reveal a creamy, tangy cream cheese center, perfectly complementing the sweet and spiced carrot and zucchini muffin.