Preheat your oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners.
Lightly mist the liners with cooking spray to prevent sticking.
In a medium bowl, whisk the flour, protein powder, baking powder, baking soda, salt, and cinnamon. Set aside.
In a large bowl, whisk the eggs, Greek yogurt, oil, maple syrup, milk, vanilla, and lemon zest until smooth. Don’t overmix.
Add the dry ingredients to the wet bowl. Fold gently with a spatula until just combined. A few small lumps are fine.
Toss blueberries with 1 teaspoon flour, then fold into the batter. Reserve a few berries for the tops if you like a pop of color.
Make the cheesecake swirl: In a small bowl, beat cream cheese, Greek yogurt, maple syrup, vanilla, and a pinch of salt until creamy and smooth.
Fill each muffin cup about 2/3 full with batter.
Add a spoonful (about 1 teaspoon) of cheesecake mixture on top of each. Use a toothpick or butter knife to gently swirl.
Top with a few extra blueberries if reserved. Bake 16–20 minutes, or until a toothpick inserted into a muffin (avoiding the cheesecake pocket) comes out with just a few moist crumbs.
Cool in the pan for 5 minutes, then transfer to a wire rack. Let them cool fully so the cheesecake swirl sets.