Preheat your oven to 375°F. Line a 12-cup muffin pan with paper liners. Lightly spray the liners if desired. This helps the muffins release easily and keeps the edges nicely golden.

Place softened cream cheese in a bowl. Add sugar, egg yolk, vanilla, and flour. Beat until completely smooth and creamy. Set the filling aside while you prepare the pumpkin muffin batter.

In another bowl, whisk pumpkin puree, sugar, brown sugar, oil, eggs, and vanilla. Mix until smooth and well combined. The mixture should look creamy without any large lumps or streaks.

Add flour, baking soda, baking powder, pumpkin pie spice, cinnamon, and salt to another bowl. Whisk everything together evenly. This helps distribute the spices and leavening ingredients throughout the muffin batter.

Slowly add the dry ingredients to the pumpkin mixture. Stir gently with a rubber spatula until just combined. Do not overmix the batter. A few small streaks are better than a tough muffin.

Spoon a small amount of batter into each muffin liner. Add about one tablespoon of cream cheese filling in the center. Cover the filling with more pumpkin batter until each cup is nearly full.

For the optional topping, mix brown sugar, flour, and cinnamon. Cut in cold butter using your fingers or a fork. Continue until coarse crumbs form. Sprinkle the mixture evenly over each muffin.

Place the muffin pan in the preheated oven. Bake for 20 to 22 minutes. Check the pumpkin portion with a toothpick. Avoid the cream cheese center when testing for doneness.

Let the muffins cool inside the pan for about five minutes. Transfer them carefully to a wire rack. Allow them to cool further before serving. This helps the cream cheese center set properly.