Place a rack in the centre of your oven and preheat oven to 375ºF.
In a large bowl, combine the whole wheat pastry flour, quinoa flour, baking soda, salt, cinnamon and nutmeg.
In a separate bowl, add the sugar, oil, yogurt, eggs, vanilla extract and mashed bananas, whisk together until well combined.
Add the wet mixture to the dry ingredients and fold batter with rubber spatula until just combined.
Add the chocolate chips and fold in. Don't over-mix the batter or you will have tough muffins.
Spoon the batter into the greased or paper-lined muffin cups distributing the batter evenly over 12 muffin cups.
Bake at 375ºF for 5 minutes and then reduce heat to 350ºF and continue to bake for 13 to 15 minutes more. To test for doneness, insert a toothpick in the centre of a muffin, if it comes out clean or with a few crumbs the muffins are done.
Remove the muffins from the oven and let them cool in the pan on a rack for 5 minutes.
Remove the muffins from the pan and place onto a wire rack to cool.
Store the muffins in an airtight container at room temperature for two to three days. For longer storage keep in the fridge or you can also freeze them for later consumption.