Preheat oven to 350F. Using either homemade parchment paper liners or regular store-bought, line every other muffin tin. You'll bake in two batches, but if you have two pans, you can bake all at once!
In a bowl, whisk the flour and baking soda. Set aside.
In a large bowl, beat the sugars, eggs, and olive oil for 1-2 minutes.
Add the pumpkin puree, pumpkin spice, and vanilla. Mix well, then fold in the flour mixture just until incorporated.
Divide the batter between the 12 muffin liners.
In either a separate bowl or the bowl of a stand mixer, beat the softened cream cheese, maple syrup, flour, and milk until smooth.
Pipe 1/2 tablespoon dollops in the centers of each muffin, then top with pumpkin seeds.
Bake for 20-25 minutes, until a toothpick inserted into the centers comes out clean.
Let cool in the pan at least 5 minutes before enjoying!