Preheat your oven to 350°F (175°C). Line two baking trays with parchment paper. This helps prevent sticking and makes it easier to remove the soft pumpkin cakes without breaking them.
In a medium bowl, whisk together the flour, baking powder, baking soda, cinnamon, ginger, nutmeg, and salt. Set aside.
In a large bowl, whisk the pumpkin puree, brown sugar, granulated sugar, vegetable oil, egg, and vanilla extract until smooth. Make sure the sugar is evenly incorporated into the pumpkin mixture.
Gradually add the dry ingredients to the wet ingredients. Stir gently until the flour is just incorporated. The batter should be thick enough to hold its shape when scooped. Avoid overmixing, which can make the cakes dense.
Using a tablespoon or small cookie scoop, place rounded portions of batter onto the prepared trays, leaving approximately 2 inches between them. Aim for similar sizes so the cakes can be paired evenly after baking.
Bake for 12–15 minutes, or until the tops look set and spring back gently when touched. A toothpick inserted into the center should come out clean or with a few moist crumbs. Avoid overbaking to maintain a soft, cake-like texture.
Allow the cakes to rest on the baking trays for about 5 minutes before transferring them to a wire rack. Cool completely before adding the filling; warm cakes can cause the cream cheese mixture to melt.
In a mixing bowl, beat the softened cream cheese and butter until smooth and creamy. Gradually add the powdered sugar, then mix in the vanilla extract and optional cinnamon. Beat until the filling is fluffy but firm enough to hold its shape.
Pair the cooled cakes by similar size. Spread or pipe a generous layer of cream cheese filling onto the flat side of one cake, then gently press another cake on top to form a sandwich. Repeat with the remaining cakes and filling.
Place the assembled whoopie pies in the refrigerator for about 20–30 minutes to help the filling set. Serve chilled or allow them to sit at room temperature briefly before serving for a softer texture. Keep any leftovers refrigerated because of the cream cheese filling.