Reduce the cider: In a small saucepan, simmer 1 cup apple cider over medium heat for 15–20 minutes, stirring occasionally, until it reduces to about ⅓ cup. Cool slightly.
Preheat oven to 350°F (175°C). Grease a mini muffin pan.
In a medium bowl, whisk together almond flour, tapioca flour, coconut flour, baking powder, baking soda, salt, cinnamon, nutmeg, and sugar.
In another bowl, whisk eggs, reduced cider, melted coconut oil, milk, and vanilla until smooth.
Stir wet ingredients into dry until just combined. Batter will be thick.
Scoop about 1 tbsp batter into each mini muffin well (fills ~18–20).
Bake 11–13 minutes, until lightly golden and a toothpick comes out clean.
Cool for 5 minutes, then brush or dip each donut hole in melted coconut oil/butter and roll in the cinnamon sugar mix.