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Preheat the oven to 350 degrees F.
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In a large mixing bowl, whisk together the flour, sugar, baking soda, baking powder, and salt.
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Use your fingers to work the cold butter into the flour mixture until it resembles a fine meal.
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In a small bowl, whisk together the buttermilk, egg, vanilla, and pomegranate seeds. Add the wet to the dry, mix well.
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Grease two mini doughnut baking pans. Add the batter to a plastic sealable sandwich bag. Seal the bag and cut one of the corners of the bag off. Pipe the batter into the greased pans. Fill each cavity about ½ the way.
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Bake the doughnuts for fifteen minutes until golden around the edges.
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While the doughnuts bake, whisk together powdered sugar, milk, and pomegranate juice. Note: Just slightly squeeze a quarter of a pomegranate and the juice will release.
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Let the doughnuts cool slightly before dipping them into the glaze. Place the glazed doughnuts on a wire rack with a paper towel underneath. Top doughnuts with pomegranate seeds and coconut flakes while the glaze is still slightly wet. Serve immediately.