Preheat the oven to 350°F and line two large baking sheets with parchment (or grease with cooking spray).
In a large bowl, whisk together the whole wheat flour, wheat germ, and flax seed. In a separate bowl, whisk the eggs, olive oil, applesauce, pumpkin, and honey until smooth.
Add the wet ingredients to the dry ingredients and stir until thoroughly combined. Form the dough into a disc.
On floured parchment paper, roll the dough out to 1/4-inch thick. Cut shapes with a cookie cutter and place them an inch apart on the prepared baking sheets.
Bake for 25-30 minutes, or until the treats are deep golden brown and very hard. Cool completely on a rack before letting your pup enjoy.
Notes
If the dough is sticky or hard to work with, refrigerate it for 30 minutes and/or knead in an extra tablespoon or two of flour.