Preheat and prep: Heat your oven to 350°F (175°C).
Line a 12-cup muffin pan with liners or lightly grease each cup.
Whisk dry ingredients: In a large bowl, whisk 1 1/2 cups flour, 1/2 cup protein powder, 1 1/2 teaspoons baking powder, 1/2 teaspoon baking soda, 1/2 teaspoon fine sea salt, and 1/2 teaspoon cinnamon.
Mix the wet ingredients: In a separate bowl, whisk 2 large eggs, 3/4 cup Greek yogurt, 1/3 cup milk, 1/3 cup neutral oil, 1/2 cup coconut or brown sugar, and 1 teaspoon vanilla until smooth.
Combine: Pour the wet mixture into the dry ingredients. Stir gently with a spatula until just combined. The batter should be thick but scoopable.
Avoid overmixing.
Add caramel: Warm 1/3 cup caramel sauce slightly so it’s pourable but not hot. Fold half of it into the batter for a light caramel flavor throughout. Do not overmix; streaks are fine.
Portion the batter: Divide batter evenly among the muffin cups, filling each about 3/4 full.
If using add-ins, sprinkle a few into each cup and gently press in.
Caramel swirl: Spoon a small dollop of the remaining caramel (about 1/2 teaspoon) on top of each muffin. Use a toothpick or knife to swirl it into the surface.
Bake: Bake for 16–20 minutes, or until the tops are set and a toothpick inserted in the center comes out with a few moist crumbs.
Finish with salt: While warm, sprinkle a tiny pinch of flaky sea salt on each muffin. This brings out the caramel flavor without making them salty.
Cool: Let muffins rest in the pan for 5 minutes, then transfer to a wire rack to cool completely.
This helps set the structure so they don’t sink.