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Heat olive oil over medium heat in a medium-sized soup pot or Dutch oven. Add 2/3 of the sliced shallots and a generous pinch each sea salt and pepper; sauté until tender and golden, about 4 minutes. Add sliced radishes and cook until radishes are translucent and tender, 7 - 10 minutes.
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Fold in potatoes, 3 beet slices, 3 bay leaves, and another generous pinch of sea salt. Stir to combine and then slowly stir in broth. Bring mixture to a gentle boil, then turn heat down to a simmer. Cook 20 minutes or until potatoes can easily be sliced with a fork.
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Fish bay leaves out and set aside. Working carefully, puree the hot soup and then return to the soup pot; reheat oven medium-low heat until soup is steamy. Levels of pinkness will vary – if you'd like to add a little more color, grate one of the remaining beet slices and squeeze juice into soup a little at a time, until the perfect pinkness is achieved. Taste soup and add sea salt and pepper as needed.
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While soup cooks, prepare the garnishes. Fill a small sauté pan with 1/2-inch of neutral cooking oil and set over medium-heat heat. You want the oil to be very hot, but not so hot that it smokes. Add a few of the remaining sliced shallots at a time and cook until light golden and crisp, 1 - 2 minutes. Use a slotted spoon to remove shallots to a paper towel-lined plate and toss with sea salt. Continue until all of the shallots have been cooked.
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To make skillet croutons, set a medium skillet over medium heat. Drizzle both sides of the bread with the remaining tablespoon olive oil, and sprinkle with a pinch of sea salt and pepper. Set in the skillet and cook until crotons are crisp and golden, about 4 minutes a side.
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Ladle soup into shallow bowls and garnish with a line of crispy shallots, fresh ground pepper, a bay leaf, and a crouton. Serve immediately.