Preheat the oven to 350 degrees. Line a large baking pan with parchment or a silicone baking mat. Set aside.
In a large bowl, whisk together almond flour, rolled oats, ground flax, baking soda and sea salt until well-combined. Be sure that there are no lumps of almond flour.
Add honey, yogurt, coconut oil, egg, and vanilla extract. Stir until fully incorporated.
Stir in mini semi-sweet chocolate chips, or other add-ins. The batter will stiffen up a bit as it sits and the ingredients absorb the moisture.
Using a standard sized spring-loaded cookie scoop (or a large serving spoon), scoop cookie dough mounds onto prepared baking sheet leaving at least 3 inches between each as they will puff and spread a bit.
Bake for 14-16 minutes until puffed and golden. Remove from oven and allow to cool for 10-15 minutes before removing from pan -- they will be soft right out of the oven and will become easier to handle as they cool.