Preheat the oven to 350°F (175°C) and grease two 8-inch round cake pans.
In a large bowl, whisk together flour, cocoa powder, baking powder, baking soda, salt, cinnamon, and nutmeg.
In another bowl, mix granulated sugar, pumpkin puree, vegetable oil, eggs, milk, and vanilla extract until well combined.
Gradually add dry ingredients to the wet ingredients, stirring just until combined.
Divide the batter evenly between the prepared cake pans.
Bake for 25-30 minutes or until a toothpick inserted into the center comes out clean. Let cool completely.
For the ganache, melt chocolate chips in a heat-safe bowl over simmering water, stirring until smooth, then let it cool slightly.
Spread ganache between the cake layers and over the top. Serve the cake at room temperature.