Preheat the oven to 350º. Line a muffin tin with cupcake wrappers or spray each muffin cup with non-stick cooking spray.
Rinse blueberries and pat dry. Set aside.
In a medium bowl, whisk together both flours, baking powder, baking soda, and salt. Set aside.
In another bowl, whisk together the eggs, vanilla, agave (or sugar) and yogurt. Add in lemon juice. Mix until mixture is smooth.
Alternate adding the flour mixture and milk to the egg mixture, starting and ending with the the flour mixture. Stir just until ingredients are combined. Gently fold in blueberries and lemon zest. The batter will be thick.
Fill each muffin cup about 3/4 of the way full. Bake muffins for 15-20 minutes until top is firm or a toothpick comes out clean. Let muffins cool for about 10 minutes before removing them from the pan.