Preheat the oven to 350°F (175°C).
Line two baking sheets with parchment paper.
Bring the egg to room temperature for better mixing. If using a flax egg, mix 1 tablespoon ground flax with 2.5 tablespoons water and let it gel for 10 minutes.
Whisk dry ingredients: In a medium bowl, whisk 1 cup almond flour, 3/4 cup oat flour, 1/2 cup whole-wheat pastry flour, 1/2 teaspoon baking soda, and 1/2 teaspoon fine sea salt. Break up any almond flour clumps.
Cream sugars and oil: In a large bowl, stir 1/2 cup coconut sugar with 1/3 cup softened coconut oil (or avocado oil) until glossy and combined. Add 2 tablespoons maple syrup and 2 teaspoons vanilla; mix until smooth.
Add the egg: Beat in 1 room-temp egg (or the flax egg) until the mixture looks cohesive and slightly thick.
Combine: Fold the dry ingredients into the wet with a spatula. The dough should feel soft but not sticky.
Stir in chocolate: Fold in 3/4 to 1 cup dark chocolate chips or chunks. Save a few for topping.
Chill briefly: Cover and chill the dough for 20–30 minutes. This step gives thick, chewy cookies.
Scoop: Use a 1.5-tablespoon scoop to portion 12–14 mounds onto prepared sheets, spacing 2 inches apart. Press a few extra chips on top.
Bake: Bake 8–10 minutes until edges set and centers look slightly underdone. Rotate the pans halfway.
Finish: Sprinkle flaky salt. Cool on the sheet 5 minutes, then transfer to a rack. They firm up as they cool.
Don’t overbake: Pull them when centers still look soft for fudgy middles.
Weigh flours if you can: Too much flour dries cookies. Lightly spoon and level if using cups.
Mind your oil: Coconut oil should be soft, not melted. Melted oil can make cookies spread too much.
Room-temp egg: Cold eggs tighten dough and reduce spread.
