Preheat oven to 350Ëš F. Line a baking sheet with parchment paper.
Process whole almonds in a food processor until finely ground. Transfer to bowl and add flour, baking powder, and salt. Whisk until combined.
Combine the ground flax seed with the water in a small bowl or glass measuring cup. Mix well and let sit until a thick gel forms. This creates a binder to replace eggs.
Using an electric hand mixer, add honey, oil, and vanilla to the chia/water gel and mix well. Add the wet ingredients to the dry ingredients and mix well.
Roll Tablespoons of dough into 1-inch balls and place on prepared baking sheets. Press the tip of your finger into the center of each cookie to make an indentation. Bake the cookies until set and slightly golden on the bottom, 10-12 minutes. Let cool completely on a wire rack.
Combine 2 Tablespoons honey and 1 Tablespoon almond butter and mix well. Fill each cookie with about 1/4 teaspoon and top with almonds if desired. Enjoy!