Preheat oven to 425°F (220°C) and line a 12-cup muffin pan with paper liners. Mix streusel flour, brown sugar, cinnamon, and melted butter with a fork until crumbly; chill until ready to use.
Whisk flour, baking powder, baking soda, cinnamon, and salt in a large bowl. In a second bowl, whisk melted butter, brown sugar, granulated sugar, eggs, Greek yogurt, milk, and vanilla.
Toss diced fresh apples with 1 tablespoon flour, then fold the wet mixture and apples into the dry ingredients just until combined.
Divide batter among the 12 muffin cups, top generously with chilled streusel, and bake at 425°F for 5 minutes. Reduce oven temperature to 350°F (175°C) and bake for 14–16 minutes more until golden and a toothpick comes out clean.