Preheat oven to 350 degrees.
Line 12 muffin tin cups with liners.
Sift the flour, sugar, baking powder, salt, cinnamon, and nutmeg together into a medium bowl. Make a well in the center.
Place the egg, melted butter, and milk in the well. Stir with a wooden spoon just until all ingredients are combined. Quickly stir in the raspberries and lemon zest. Fill each muffin cup three fourths full with the batter.
Combine the pecans, brown sugar, flour, cinnamon, and lemon zest in a small bowl. Pour in the melted butter and mix. Sprinkle the mixture evenly over the top of each muffin.
Bake until browned and firm 15 - 18 minutes.