In a large bowl, beat butter until light and creamy. Add sugars and beat until well combined. Mix in pumpkin butter and vanilla and beat until well combined. In a separate bowl, combine flours, baking soda, salt and spices. Add dry ingredients, and chocolate chips, to wet ingredients, and mix until just combined. Cover bowl tightly and place in the refrigerator to chill for 30 to 60 minutes.
When ready to bake, preheat oven to 325 degrees F.
Scoop cookie dough using a cookie scoop onto a baking sheet lined with a silicone baking mat. Bake for approximately 8-9 minutes. They will be slightly underbaked when you remove them from the oven. Allow to cool completely on the pan before removing with a spatula. Store in an airtight container.
*Tip - to keep cookies moist and soft, store them with a piece of white sandwich bread in their container!