Heat your oven to 350°F (175°C) and place paper liners in a 12-cup muffin tin.
Fry the bacon until it's crisp, drain on paper towels, then crumble it, reserving some pieces to top the muffins.
In a large bowl, whisk together the Greek yogurt, eggs, maple syrup, milk, and vanilla extract until the mixture is smooth.
In another bowl, mix the whole wheat flour or oat flour, vanilla protein powder, baking powder, baking soda, and salt.
Gently fold the dry ingredients into the wet ingredients just until blended; lumps are fine to keep the muffins fluffy.
Stir in the crumbled bacon, keeping some aside for later.
Spoon the batter into the muffin cups, filling each about two-thirds full.
Scatter the reserved bacon pieces over the tops of the muffins.
Bake for 18 to 22 minutes, or until the muffins turn golden and a toothpick inserted in the center comes out clean.
Let the muffins cool for 5 minutes in the pan before transferring them to a wire rack to finish cooling.