In the bowl of a stand mixer, beat the cream cheese and powdered sugar together until creamy and smooth, about 2 minutes. Scrape down the sides as needed to ensure there are no lumps in the filling.
In a medium mixing bowl, whisk together the all-purpose flour, packed dark brown sugar, baking powder, baking soda, 1 1/2 teaspoons ground cinnamon, kosher salt, and ground nutmeg until evenly mixed. This ensures that the leavening agents and spices are distributed throughout the flour.
In a large mixing bowl, whisk together the pumpkin purée, whole milk, melted unsalted butter, and large eggs until the mixture is smooth and thoroughly combined.
Slowly fold the dry ingredients from Step 2 into the wet mixture from Step 3. Stir gently, just until combined – do not overmix, as this helps keep the waffles tender.
Preheat your waffle iron and brush it with melted butter to prevent sticking. Spoon a thin layer of pumpkin batter (from Step 4) onto the waffle maker, spreading it to cover the surface. Drop about 2 tablespoons of the cream cheese filling (from Step 1) over the batter, then add another layer of pumpkin batter on top to sandwich the filling. Close the iron and cook until golden brown, following your waffle maker’s instructions. Repeat with the remaining batter and filling. I like to sprinkle a little extra cinnamon on top before closing the iron for an even warmer flavor.
Transfer cooked waffles to a plate and serve warm. Top with additional butter, a sprinkle of extra cinnamon if desired, and plenty of maple syrup. Enjoy your fluffy pumpkin cream cheese waffles!