Preheat oven to 425°F (218°C). Spray a 12-count muffin pan with nonstick spray or line with cupcake liners.

In a small bowl, mix the brown sugar, cinnamon, and melted butter until combined. Add the flour and mix until crumbs form. Set aside.

In a large bowl, whisk the flour, baking powder, baking soda, salt, cinnamon, and pumpkin pie spice together. Set aside.

In a medium bowl, whisk the brown sugar, granulated sugar, eggs, pumpkin, oil, milk, and vanilla extract together. Pour the wet ingredients into the dry ingredients and mix until just combined.

In a medium bowl, beat the cream cheese on medium-high speed until smooth. Beat in the egg yolk, vanilla extract, and sugar until combined.

Spoon 1 heaping tablespoon of pumpkin muffin batter into the muffin cups. Layer with about 1 spoonful of cheesecake filling, then add another heaping tablespoon of muffin batter to fill the cups.

Sprinkle crumb topping onto each muffin and press it down into the tops.

Bake for 5 minutes at 425°F (218°C), then reduce heat to 350°F (177°C) and continue baking for another 15-17 minutes. Allow to cool for at least 10 minutes in the pan before serving.

Cover leftover muffins tightly and store at room temperature for up to 2 days or in the refrigerator for up to 1 week.