Preheat oven to 350 degrees F (180 degrees C). Spray mini muffin pan with coconut oil cooking spray or line with mini liners.
Add Spelt Flour (3/4 cup), Whole Wheat Flour (3/4 cup), Pumpkin Pie Spice (1 tablespoon), Baking Soda (1 teaspoon), Baking Powder (1/4 teaspoon), and Salt (1/2 teaspoon) to medium bowl, whisk until combined.
Add Organic Egg (2), Raw Honey (1/4 cup) and Brown Sugar (1/4 cup), stir to mix, then add Butter (1/3 cup) and continue stirring until combined.
Stir inButternut Squash (3/4 cup) and Nonfat Plain Greek Yogurt (1/4 cup), then fold in Dark Chocolate Chips (1/2 cup), batter should be fairly thick.
Add batter to muffin pan, evenly distributed, then bake for 10-11 minutes or until olden brown on top and a toothpick comes out clean.
Store leftovers in an airtight container at room temperature.