For the muffins:
2 cups (9 ounces) all-purpose flour
2 teaspoons cinnamon
1 teaspoon baking powder
1/2 teaspoon baking soda
1/2 teaspoon fine sea salt
1/4 teaspoon ground ginger
1/4 teaspoon freshly ground nutmeg
2 large eggs, room temperature
1 cup packed dark brown sugar
8 ounces crème fraîche (or full-fat sour cream)
1 teaspoon pure vanilla extract
1/2 cup (4 ounces) unsalted butter, melted and still warm
2 medium-sized baking apples, peeled, cored and diced into irregular pieces (See Recipe Note)
For the streusel:
3/4 cup all-purpose flour
1/4 cup packed dark brown sugar
1/4 cup granulated sugar
1/4 teaspoon fine sea salt
1/4 cup (2 ounces) unsalted butter, melted
Preheat oven to 400°F. Grease a regular-sized muffin tin generously with cooking spray, both inside the cups and over the top.
Whisk together flour, cinnamon, baking powder, salt, ginger, and nutmeg. In another bowl, combine eggs, brown sugar, crème fraîche, and vanilla. Add the melted butter, pouring in a slow and steady stream, while whisking vigorously to emulsify the mixture.
Add the liquid mixture to the dry ingredients and gently fold until the liquid is just barely combined, being careful not to over-mix. (A few lumps are okay.) Stir in the chopped apples. Fill each muffin well all the way to the top with batter; set aside while preparing the streusel.
For the streusel, add the flour, brown sugar, sugar, and salt in a medium bowl. Pour in the melted butter and gently stir with a fork until well combined and small pebble-sized pieces remain throughout.
Top each filled well with a heaping tablespoon of streusel, lightly pressing it into the batter. (A round cookie cutter placed over the cup helps keep the mess to a minimum.) Bake muffins for 18 to 22 minutes, until tops are golden and a toothpick comes out clean. Leave the muffins in the pan for 10 to 15 minutes, then transfer to a wire rack to continue cooling.
The muffins can be stored in an airtight container for up to three days. The batter can be made in advance and held in the refrigerator for up to 2 days, or frozen for 2 weeks (thaw overnight in the fridge before using.)