Make the Quinoa
Soak the quinoa in 1 cup water for 12-24 hours
Drain and rinse the quinoa
Add the quinoa to a small pan, along with a small pinch of fine-grain sea salt and enough water to cover it by an inch or two.
Bring to the boil over high heat.
Reduce heat to low, cover pan and simmer for 15 minutes, or until all water is absorbed.
Remove from heat and allow to sit, covered, for ~ 10 minutes and fluff with a fork.
Measure out ½ cup and set aside. Save a remaining couple of tablespoons of quinoa to sprinkle over muffins
Make the Muffins
Preheat oven to 350 F.
Line a regular muffin pan with 10 paper liners.
Place flax and nut milk in a medium bowl and whisk to combine. Set aside to thicken while you cook the onion.
Warm 1 Tbsp olive oil in a skillet over medium heat.
Add the onion and sauté for 5 minutes, or until golden brown.
Add the sage, thyme, and a pinch fine-grain salt; reduce heat to low and continue cooking for another 5 minutes or until the onions have caramelized.
Remove from the heat and set them aside.
Sift flour, baking powder, and baking soda into another medium bowl. Whisk to combine and set aside.
Add the sweet potato, water, vinegar, tamari, and remaining ½ tsp fine-grain sea salt to the flax-nut milk mix and whisk until smooth.
Add ¼ cup olive oil; whisk again and add the flour mix. Stir gently until almost combined, and fold in cooked quinoa and onions.
Divide batter between the lined muffin cups, filling them to the top. Garnish each muffin with a thyme sprig and a sprinkle of remaining cooked quinoa.
Bake 45 to 50 minutes or until a toothpick inserted in the center comes out clean.
Remove from oven; leave muffins in the pan for 5 minutes before transferring them to a wire rack to cool slightly before serving.
Once cool, any leftover muffins can be stored in an airtight container in the fridge.