Preheat the oven to 325 degrees. Line a baking sheet with parchment paper.
In a medium bowl whisk together spelt flour, baking soda, and salt; set aside.
Using a whisk, beat the melted butter and brown sugar until combined. It will turn into a caramel color(1-2 minutes). Mix in the vanilla and flax "eggs" until combined (about 30 seconds).
Using a spatula, slowly add the dry ingredients and mix until just smooth (about 45 seconds).
Mix in the chocolate chips, peanut butter chips, and walnuts bits.
Using a small scoop portion out 12 cookie dough balls onto each baking sheet. Space dough balls 2 inches apart.
Bake until the edges are golden but the centers are still soft and puffy for 12 minutes). Repeat with the rest of the batter to make 2 dozen cookies.
Let the cookies cool on the baking sheets for 10 minutes, then serve warm or transfer parchment paper and cookies to a wire rack to cool completely.