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Wash and wrap 3 large beets in aluminum foil and bake for 4 hours at 325°F and the let cool while still wrapped in the foil. The skin should peel off easily as you unwrap the foil (use gloves to prevent staining your hand red!) Finely grate the beets and reserve for later.
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Whisk or sift the dry ingredients together in a large bowl, and set aside.
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Using a hand or stand mixer, start by creaming the butter & sugar together until it becomes fluffy and lightens in colour (3-5 min).
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Add the vanilla and continue mixing until well incorporated.
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Next, incorporate each egg, being sure the first is well combined before adding the second.
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Mix in the grated beets, the vinegar and milk until well combined.
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Add 1/2 of the dry ingredients and mix gently until incorporated and then add 2 tbsp boiling water and continue alternating between the dry ingredients and boiling water, being careful not to over mix.
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Preheat the oven to 350°F and line 2 muffin tins with cupcake papers.
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Use an ice cream scoop or spoon to fill the muffin molds about halfway and bake for 16-18 min or until a tooth pick test comes out clean.
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Let cool before icing.