Preheat oven to 375°F (190°C). Line baking sheets with parchment paper.
In a large bowl, whisk together flour, baking soda, cinnamon, nutmeg, and salt.
In a separate bowl, combine applesauce, sugar, apple cider, egg, and oil. Mix well.
Gradually add the dry ingredients to the wet ingredients, mixing until just combined. Do not overmix.
Drop by rounded tablespoons onto the prepared baking sheets.
Bake for 10-12 minutes, or until edges are lightly golden brown.
Let cool completely on baking sheets before frosting.
For the frosting: Beat together cream cheese and butter until smooth. Gradually add powdered sugar and vanilla extract, beating until light and fluffy.
Spread frosting on the bottom of half of the whoopie pies. Top with remaining whoopie pies to create sandwiches.
Notes
Store whoopie pies in an airtight container at room temperature for up to 3 days.