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Adjust an oven rack to the middle position and preheat the oven to 350ºF. Grease two 6-cavity doughnut pans with nonstick cooking spray, melted coconut oil, or melted butter.
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Whisk the coconut sugar, coconut flour, tapioca starch, baking powder, nutmeg, and salt together in a medium mixing bowl. Add the melted coconut oil, eggs, milk, and vanilla and whisk until smooth. The batter will be thick.
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Spoon the batter into the prepared pans, filling the cavities about three-quarters full. (If you have a piping bag and large plain pastry tip kicking around the kitchen, use those instead.) Lightly tap the pans on the counter to settle the batter.
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Bake the doughnuts until they are golden brown and spring back to the touch, about 15 minutes.
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Allow the doughnuts to cool in the pans on a wire rack for 5 minutes, then turn them out onto the rack to cool completely.
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Doughnuts are best enjoyed the day they are baked. Freeze leftovers, wrapped in plastic wrap and placed in a freezer container, for up to one month.