Preheat your oven to 350°F (175°C) and line a muffin tin with cupcake liners.
In a large mixing bowl, whisk together almond flour, coconut flour, granulated erythritol, unsweetened cocoa powder, baking powder, baking soda, and salt.
In a separate bowl, beat the eggs, then mix in the melted butter, vanilla extract, and apple cider vinegar until well combined.
Gradually add the dry ingredients to the wet mixture, stirring continuously. Slowly pour in the almond milk and red food coloring, mixing until you achieve a smooth, uniform batter.
Divide the batter evenly among the cupcake liners, filling each about two-thirds full.
Bake in the preheated oven for 18 minutes, or until a toothpick inserted into the center comes out clean.
While the cupcakes are baking, prepare the cream cheese frosting. Using an electric mixer, beat together the softened cream cheese, powdered erythritol, softened butter, and vanilla extract until smooth and creamy.
Once the cupcakes are done, remove them from the oven and allow them to cool completely before frosting.
When the cupcakes are cool, use a piping bag or a knife to frost them with the cream cheese frosting.
Serve immediately or store in an airtight container in the refrigerator.