Preheat oven to 350 degrees. Line two 12-cup standard muffin trays with paper liners and set aside.
In a small bowl, combine the dry ingredients (flours, baking powder and soda, salt and spices). Set aside.
In a small saucepan, melt the butter over medium heat. Stir frequently, and let it cook and bubble until the milk solids turn brown. Pour into a large heat-proof mixing bowl. Add the sucanat (find out more…) or brown sugar and mix. Next mix in the pumpkin puree. Add the maple syrup, then whisk in the eggs until well combined.
Fold in the flour gently, do not overmix, but make sure it is thoroughly combined. Stir in the chocolate chips, then using a measuring cup or an ice cream scoop, fill the cups 2/3 full.
Bake until the tops are firm to the touch and the muffins are slightly browned, about 20 minutes. Remove from the oven and let cool in the muffin trays, or remove to racks.