Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease with cooking spray.
In a large bowl, whisk together almond flour, gluten free oat flour, vanilla protein powder, baking powder, baking soda, and salt until well combined.
In a separate medium bowl, beat the eggs. Add Greek yogurt, honey, almond milk, and vanilla extract. Mix until smooth.
Pour the wet ingredients into the dry ingredients and gently fold together until just combined. Do not overmix.
Fold in the fresh blueberries carefully to distribute evenly.
Divide the batter evenly among the 12 muffin cups, filling each about 3/4 full.
Bake in the preheated oven for 18 to 20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Remove muffins from the oven and allow to cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.