Line two cookie sheets with a Silpat baking mat or parchment paper.
In a medium bowl, whisk together almond flour, amaranth, arrowroot flour, baking soda, salt, shredded coconut, and nutmeg until fully combined.
Using a hand mixer, beat the coconut oil, coconut sugar, egg and vanilla in a large bowl on medium until fully incorporated and smooth (roughly 2 minutes). Use a spatula to scrape down the bowl and mix again.
Add chocolate chips and walnut pieces, using spatula to combine. Refrigerate for 20 minutes. Preheat your oven to 350 F.
Using a small ice cream scoop, scoop cookie dough and drop onto prepared cookie sheets. Leave a space between them as the cookies will spread.
Bake for 8-10 minutes until the bottoms and edges are golden and tops look firm.
Let cool on the cookie sheet for a couple of minutes before transferring to wire racks (give them time to firm up). Serve immediately if you like a crisp on the outside, gooey in the center cookie. Or store in an airtight container for 3-4 days on countertop. These cookies can be frozen too if you don't plan on eating them within a few days.