Preheat oven to 375 degrees F (190 degrees C). Line 24 muffin cups with paper muffin liners.
Spread quinoa onto a baking sheet and toast in preheating oven until lightly browned, about 5 minutes.
Pour toasted quinoa into a blender and pulse until the quinoa has the consistency of cornmeal.
Stir ground quinoa, pumpkin puree, milk, water, whole wheat flour, flaxseed meal, egg, honey, coconut oil, walnut oil, chia seeds, cinnamon, baking powder, ground ginger, and salt together in a large mixing bowl until smooth. Rest mixture until chia seeds and flaxseed meal absorb some moisture and soften, about 15 minutes.
Ladle batter into prepared muffin cups to about 3/4 full.
Bake in the preheated oven until golden and the tops spring back when lightly pressed, 30 to 40 minutes.