Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners or lightly grease it.
In a large bowl, whisk together the whole wheat flour, baking powder, baking soda, salt, and cinnamon.
In another bowl, combine the Greek yogurt, applesauce, honey (or maple syrup), eggs, and vanilla extract. Mix until smooth.
Pour the wet ingredients into the dry ingredients and stir until just combined. Be careful not to overmix.
Gently fold in the blueberries until evenly distributed.
Divide the batter evenly among the muffin cups, filling each about 2/3 full.
Bake for 18-20 minutes, or until a toothpick inserted in the center comes out clean.
Allow the muffins to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.