Preheat oven to 350 degrees F (175 degrees C). Line 4 muffin cups with paper liners.
Mix almond meal, flax seed, chia seeds, and baking soda together in a small bowl. Whisk eggs, honey, and apple cider vinegar together in a separate bowl. Stir almond meal mixture into egg mixture until batter is just mixed. Mash banana into batter and fold in blueberries. Scoop batter into the prepared muffin cups.
Bake in the preheated oven until slightly browned, about 15 minutes. Cool muffins in pan for 30 minutes.