Preheat your oven to 350°F (175°C) to ensure even baking.
In a large mixing bowl, combine coconut oil, honey, natural peanut butter, egg, and vanilla extract. Mix until smooth and well blended.
In another bowl, whisk together whole wheat flour, salt, baking soda, baking powder, wheat germ, oat bran, and ground flax seeds to evenly distribute dry ingredients.
Gradually add the dry mixture to the wet mixture, stirring until just combined. Avoid overmixing to keep cookies tender.
Fold in the peanut butter or chocolate chips into the dough to personalize your cookies.
Using a cookie scooper or spoon, drop dollops of dough onto a baking sheet lined with parchment paper, leaving space between each cookie.
Bake for 10-12 minutes until edges are golden brown; centers will be soft but will firm as they cool.
Remove cookies from oven and let cool on the baking sheet for a few minutes, then transfer to a wire rack to cool completely. Enjoy warm or store for later!