Preheat the oven to 350 F, and grease 12 muffin cups very well with nonstick spray.
Spoon 1 teaspoon quinoa into each muffin cup. Carefully tilt the pan to cover the bottom and up the sides about an inch.
Finely grate the onion and butternut squash. Stir together the remaining ingredients in a medium bowl.
Spoon into muffin cups, filling about 3/4 full.
Bake for 28-30 minutes or until firm to the touch and golden brown around the edges.
Let cool for in the pan on a wire rack for at least 10 minutes, then run a sharp paring knife around the edges to carefully help lift out the muffins. (Go slowly, they are dense!)
Serve warm or at room temperature.
Store in the fridge for up to 3 days or store in the freezer in a zip top bag and reheat for 30 seconds in the microwave before serving.