Preheat the oven to 350°F. Line two baking sheets with silicone mats.
Mix the flour, baking soda and salt together in a medium bowl. Set aside.
In the bowl of a stand mixer, beat the peanut butter, butter and both sugars for about 2-3 minutes, until light and fluffy. Mix in the egg and vanilla.
Add in the flour mixture on low speed and stir until the dough forms.
Using a cookie scoop (about 1 heaping tablespoon of dough), roll balls of dough in annatto-sugar and drop onto prepared cookie sheet. Flatten slightly and leave space for spreading.
Bake for 8 minutes, take out of the oven and top with a bagoong caramel. Return to the oven and bake for an additional 1-2 minutes, or until edges are slightly browned and the caramel is slightly melted, and remove from oven.
Let cool for 5 minutes on cookie sheets before transferring cookies to a wire rack to cool completely.
Store in an airtight container for up to 5 days.