Preheat and Prep: Preheat your oven to 325°F (163°C). Line a large baking sheet (or two standard sheets) with parchment paper or silicone baking mats to prevent sticking.

Cream the Base: In a large mixing bowl, beat the softened butter and 3/4 cup peanut butter together until smooth. Add the brown sugar alternative and beat again until the mixture is fluffy and well-incorporated.

Add Wet Ingredients: Beat in the egg and vanilla extract until fully combined.

Incorporate Dry Ingredients: Add the almond flour, peanut flour, baking soda, and fine sea salt to the wet mixture. Mix on low speed just until a cohesive dough forms.

Shape the Cookies: Scoop the dough and roll into 1-inch balls. Arrange them on the prepared baking sheets, spacing them about 2 inches apart. Gently flatten each ball with your palm to approximately 1/2-inch thickness.

Bake and Indent: Bake for 12 to 15 minutes, or until the edges are barely golden and the tops look set. Remove from the oven immediately. While the cookies are still hot, gently press the back of a rounded teaspoon into the center of each cookie to create a small well. Allow them to cool completely on the pan (they will firm up as they cool).

Make the Filling: In a small microwave-safe bowl, combine the chocolate chips and the remaining 2 tablespoons of peanut butter. Microwave in 30-second intervals, stirring in between, until fully melted and glossy.

Fill and Set: Spoon a small dollop of the chocolate mixture into the well of each cooled cookie. If desired, sprinkle a tiny pinch of flaky sea salt over the chocolate for flavor contrast. Place the cookies in the refrigerator for about 30 minutes to set the chocolate before serving.