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Pre-heat the oven to 375 degrees. Take two 12 well muffin tins and spray the first one liberally with cooking spray. The second one only needs two of the wells sprayed.
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In a large mixing bowl whisk together the quinoa flour, brown sugar, baking powder, baking soda, pumpkin pie spice, cinnamon, nutmeg, ground ginger and salt until well combined. In another bowl whisk together the canned pumpkin, milk, apple sauce, vanilla, fresh ginger and eggs.
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Pour the wet ingredients into the big bowl of dry ingredients and whisk it all together until just combined into a batter. Some lumps are ok, don't over work it. Then switch to a spatula and gently fold in the flax seeds.
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Fill each of the 14 prepared muffin wells almost to the brim with the muffin batter. Get them into the oven to bake for 20-25 minutes, until golden and a toothpick inserted into the center comes out clean.
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Take the muffins out and let them cool in the muffin tins for a few minutes, then turn them out onto a cooling rack to finish cooling enough to easily handle. Serve them warm and enjoy!