Preheat oven to 375°F (190°C). Line a 12-cup muffin pan with paper liners.
Make the filling: Beat cream cheese, powdered sugar, and vanilla until smooth. Set aside.
Mix dry ingredients: In a bowl, whisk flour, baking powder, baking soda, and salt.
Mix wet ingredients: In another bowl, whisk melted butter, sugar, eggs, vanilla, yogurt, and milk until smooth.
Combine: Slowly add dry to wet, mixing just until combined. Gently fold in the blueberries.
Fill muffin cups: Spoon batter to fill each liner halfway. Add 1–2 tsp cream cheese mixture in the center. Top with more batter to fill ¾ full. Swirl tops with a toothpick if desired.
Bake: For 20–24 minutes, or until tops are golden and a toothpick (not hitting cream cheese) comes out clean.
Cool: Let muffins sit in pan 5 mins, then transfer to a wire rack to cool completely.