Preheat an oven to 350F and place 9 silicone muffin cups on a baking sheet or spray 9 slots in a 12-muffin tin with nonstick cooking spray.
Mix the muffin ingredients together in a large bowl before folding in the blueberries. Set aside.
Microwave the cream cheese for 60 seconds before stirring in the Greek yogurt and protein powder. Mix until smooth.
Add 2 tablespoons of the muffin mixture to each of the baking cups, filling them about 1/3 full. IMPORTANT: Do your best to limit the amount of blueberries on the bottom layer to avoid a soggy bottom and have more blueberries on top after the muffins bake.
Spoon about a tablespoon of the cream cheese mixture on top of the muffin layer.
Spoon the remaining muffin mixture on top of the cream cheese layer.
Bake for 20-22 minutes or until the tops are golden brown.
Remove to cool. The muffins are best when fully cooled and refrigerated for 30-60 minutes to allow the cream cheese filling to set.