Preheat the oven to 350F and line a 12-cup muffin tin with cupcake liners.
Make the Pumpkin seed topping
Melt butter in a small pan over medium heat (about 1 minute). Add the brown sugar and pumpkin seeds and cook, stirring constantly, for 2–3 minutes until the sugar is melted and coating the seeds.
Transfer the mixture onto a lined baking sheet and let it cool completely (about 15–20 minutes) until it hardens into a crunchy, praline-like sheet. Once cooled, roughly chop into small pieces and set aside.
Make the cream cheese filling
Mix the cream cheese, sugar, milk, flour, and vanilla extract until smooth. Transfer to a piping bag or a zip-top bag with the corner snipped and set aside.
In a medium bowl, sift together all the dry spices (cinnamon, cloves, nutmeg, allspice, ginger), baking soda, and salt with the flour. Whisk everything together until evenly combined.
In a separate, larger bowl, combine the sugars, oil, the pumpkin puree, vanilla extract, and eggs and whisk until smooth.
3/4 cup granulated sugar, 1/2 cup canola oil, 1 cup canned pumpkin, 2 large eggs, 1 tsp vanilla extract, 1/4 cup brown sugar
Pour the dry ingredients into the wet mixture. Using a spatula or large spoon, fold everything together gently. The batter should be uniform, but it’s okay if there are a few streaks of flour, don’t overmix! Overmixing can make the muffins dense. The batter should be thick but scoopable , it should hold its shape when scooped into the muffin liners, not runny.
Scoop the batter into the lined muffin cups, filling each about three-quarters full. Insert the tip of the cream cheese bag about 1 cm into the center of each muffin and squeeze gently while pulling up to create a small cream cheese pocket. Sprinkle the chopped pumpkin seed praline over the top, avoiding the cream cheese center.
Bake for 18-20 minutes, or until a toothpick inserted near the edge comes out clean. Let muffins cool in the pan for a few minutes, then transfer to a wire rack.
Notes
How to store pumpkin cheesecake muffins
Since these pumpkin muffins have cream cheese in the center, it is preferable to keep them stored in an air-tight container in the fridge.They will last for up to 4 days this way. Once you're ready to enjoy them you can have them as is, straight out of the fridge. Warmed up for a few seconds in the microwave or the oven, or even just at room temperature. This will depend on your personal preference.