Prepare the oven and baking sheets. Preheat the oven to 375 degrees F (190 degrees C). Line two large baking sheets with parchment paper.
Cream the butter and sugars. Add the softened butter, brown sugar, and granulated sugar to a large mixing bowl. Beat with a hand mixer for 2-3 minutes, or until light and fluffy, stopping as needed to scrape down the sides of the bowl.
1 cup butter, ½ cup brown sugar, ¾ cup granulated sugar
Add the eggs and vanilla. Beat in the eggs one at a time, mixing well after each addition. Add the vanilla extract and mix until combined.
3 large eggs, 1 tablespoon vanilla extract
Combine the dry ingredients. In a separate large bowl, whisk together the all-purpose flour, whole wheat flour, rolled oats, baking soda, salt, cinnamon, and pumpkin pie spice.
1½ cups all-purpose flour, 1 cup whole wheat flour, 3 cups old fashioned rolled oats, 1 teaspoon baking soda, ½ teaspoon salt, 1 teaspoon ground cinnamon, 2 teaspoons pumpkin pie spice
Add the pumpkin and dry ingredients. Using a wooden spoon or rubber spatula, alternate adding the dry ingredients and pumpkin puree to the butter mixture. Start with one-third of the dry ingredients, followed by half of the pumpkin. Add another third of the dry ingredients, the remaining pumpkin, and finally the remaining dry ingredients. Mix gently between each addition, just until combined.
1 (15 ounce) can 100% pure pumpkin puree
Add the chocolate and flaxseeds. Fold in the chocolate chips and whole toasted flaxseeds until evenly distributed throughout the dough.
1½ cups semi-sweet chocolate chips, ⅓ cup whole toasted flaxseeds
Scoop and shape. Scoop large spoonfuls of cookie dough onto the prepared baking sheets, leaving a little space between each cookie. Since these cookies don't spread very much, gently flatten the tops with the back of a spoon.
Bake. Bake for 10-14 minutes, or until the cookies are set around the edges but remain soft in the center.
Cool. Remove from the oven and, if desired, immediately press a few additional chocolate chips into the tops. Let the cookies cool on the baking sheet for 5 minutes before transferring them to a wire rack to cool completely.