Prep the pan and oven. Heat your oven to 350°F (175°C).
Line a 12-cup muffin tin with paper liners or lightly grease it.
Mix the dry ingredients. In a large bowl, whisk together oat flour, protein powder, baking powder, salt, and cinnamon. Break up any clumps so the batter stays smooth.
Combine the wet ingredients. In another bowl, whisk Greek yogurt, eggs, applesauce, milk, maple syrup, vanilla, and melted oil until creamy.
Bring it together. Pour the wet mixture into the dry. Stir gently with a spatula just until combined.
The batter should be thick but scoopable. If it seems dry, add a tablespoon of milk.
Make the cinnamon swirl. Stir brown sugar, cinnamon, melted butter, and a pinch of salt in a small bowl until it looks like wet sand.
Build the layers. Spoon about 1 heaping tablespoon of batter into each muffin cup. Add a small spoonful of the cinnamon mixture on top.
Cover with another tablespoon of batter. Swirl lightly with a toothpick for that cinnamon roll look.
Bake. Bake for 15–18 minutes, or until the tops are set and a toothpick comes out with a few moist crumbs. Do not overbake—protein muffins can dry out fast.
Cool. Let the muffins rest in the pan for 5 minutes, then move to a wire rack to cool fully.
Glaze (optional). Whisk powdered sugar, vanilla, and milk until smooth and slightly thick.
Drizzle over cooled muffins. For a lower-sugar option, skip the glaze or use a light drizzle.