Rinse quinoa in a fine strainer with cold water to remove bitterness until water runs clear and is no longer frothy.
Heat milk in a saucepan over medium heat until warm, 2 to 3 minutes. Stir quinoa and salt into the milk; simmer over medium-low heat until much of the liquid has been absorbed, about 20 minutes. Remove saucepan from heat. Stir maple syrup and lemon zest into the quinoa mixture. Gently fold blueberries into the mixture.
Divide quinoa mixture between 2 bowls; top each with 1 teaspoon flax seed to serve.