Preheat and Prepare:
Preheat your oven to 375°F (190°C) and line a muffin tin with muffin liners.
Mix Dry Ingredients:
In a large bowl, whisk together the flour, baking powder, baking soda, salt, and sugar.
Combine Wet Ingredients:
In another bowl, whisk together the melted butter, eggs, milk, lemon juice, and lemon zest until well combined.
Prepare the Batter:
Gradually add the wet ingredients to the dry ingredients, mixing until just combined. Be careful not to overmix; a few lumps are fine.
Make the Cream Cheese Filling:
In a separate bowl, beat the softened cream cheese, powdered sugar, and vanilla extract until smooth. Transfer the filling to a piping bag or set aside with a spoon for assembly.
Assemble the Muffins:
Spoon a layer of muffin batter into each liner, filling it about halfway. Add a dollop (or pipe) of cream cheese filling in the center, then top with more batter to cover the filling.
Bake:
Bake the muffins for 18–22 minutes, or until the tops are golden and a toothpick inserted near the edge comes out clean.
Cool and Serve:
Allow the muffins to cool in the tin for 5 minutes before transferring them to a wire rack. Dust with powdered sugar or drizzle with lemon glaze if desired.