Preheat your oven to 350°F (175°C) and line a baking sheet with parchment paper. Set aside.
In a medium bowl, whisk together the melted butter and brown sugar until smooth and well combined.
Add the eggs and mix until fully incorporated. Stir in the crushed pineapple.
Add the flour, cinnamon, nutmeg, baking powder, baking soda, and salt directly into the bowl. Gently fold the dry ingredients into the wet ingredients until just combined: do not overmix.
Fold in the shredded carrots until evenly distributed.
Using a large cookie scoop (about 3–4 tablespoons of dough), scoop 10 evenly sized portions onto your prepared baking sheet, spacing them a few inches apart. This recipe makes 10 large cookies.
Using the back of a spoon (or your thumb), gently create a small indent in the center of each dough mound. Place about 1 teaspoon of cream cheese into each indent.
Top each cookie with about 1 tablespoon of additional dough, gently covering and sealing the cream cheese inside.
Bake for 14–16 minutes, or until the edges are set and lightly golden. The centers may still look slightly soft: that’s perfect.
Allow the cookies to cool on the baking sheet for 5–10 minutes before transferring to a wire rack to cool completely.