Prep your pan and oven. Heat oven to 350°F (175°C).
Line a 12-cup muffin tin with paper liners or lightly grease with oil spray.
Combine dry ingredients. In a large bowl, whisk flour, protein powder, brown sugar, baking powder, baking soda, and fine sea salt until no clumps remain.
Whisk the wet ingredients. In a separate bowl or large measuring cup, whisk eggs, Greek yogurt, milk, oil, and vanilla until smooth.
Bring it together. Pour wet ingredients into the dry. Stir with a spatula just until combined. The batter should be thick but scoopable.
Do not overmix.
Add mix-ins if using. Fold in mini chocolate chips or chopped dates. Keep a few chips for the tops if you like.
Portion the batter. Divide evenly among the muffin cups, filling each about 3/4 full. Tap the pan once on the counter to settle.
Swirl the caramel. Spoon about 1/2 teaspoon of warmed caramel sauce on top of each muffin.
Use a toothpick or butter knife to gently swirl into the surface. Sprinkle a small pinch of flaky sea salt on top of each.
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.
Cool. Let muffins cool in the pan for 5 minutes, then transfer to a wire rack. Drizzle with a little extra caramel and another tiny pinch of flaky salt if desired.
Serve. Enjoy warm or at room temperature.
They’ll firm up slightly as they cool.