In a large bowl, add in the applesauce, peanut butter, and honey. Whisk until everything is combined.
Add in the eggs one at a time and whisk each one until incorporated.
Add in 4 cups of whole wheat flour. I used whole wheat pastry flour. Stir in with a spatula until all the flour is incorporated into the cookie dough. If it gets too hard to stir, use your hands.
Dust a clean surface with the remaining 1/4 cup of whole wheat flour. Press out the dough and use the remaining flour to top the dough.
Roll the cookies out and cut the cookies out using your cutter of choice.
Place on a cookie sheet and bake in the oven for 15 minutes. Let the cookies cool completely. The cookies will not be super hard. It will be slightly soft like a cookie.