Place 2 cups of the oats in a food processor and grind until it has a flour-like consistency. Place the ground oats in a large mixing bowl.
Roughly chop the apples, removing the seeds and core. Grind in the food processor until it begins to resemble apple sauce. You may need to scrape down the sides. Some chunks are okay. Scoop the apple mixture into the mixing bowl.
To the mixing bowl, add the remaining 1 cup of whole oats, cinnamon, flax seed if using, and honey. Mix to combine. Add additional oats if the mixture is too wet, and honey or water if it is too dry.
Preheat oven to 350F. If the mixture is sticky, lightly dust the surface with flour or additional ground oats. Roll out the dough to approximately 1/4" thick. Using your desired cookie cutter, cut out the treat shapes and place them on a silicone baking mat or parchment paper lined baking sheet.
Bake treats at 350F for 15 minutes. Turn off the oven, leaving the cookies inside, and let them sit for two hours. This will make the cookies crunchier. For soft cookies, remove them after the 15 minutes to cool at room temperature.
Store soft treats in an airtight container, kept in the refrigerator, for up to 2 weeks. Hard treats can be kept at room temperature up to 3 weeks.
The number of treats will vary with the thickness of the dough and size of the cookie cutter. This makes 26 treats that are 2" circles.Ground flax seeds are completely optional but a great healthy ingredient to add as they provide fiber and are anti-inflammatory. Talk to your vet for more information.Any type of oats that you have should work well.