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In a large dutch oven (or other heavy-bottomed pot with a lid), melt butter over medium-high heat. Add onion and cook until softened, about 6-8 minutes. Add garlic and cook for about 1 minute more, until fragrant. Add flour and stir with a wooden spoon until it started to become bubbly and golden brown, about 1-2 minutes. Add potatoes, vegetable stock, thyme, bay leaves, salt and pepper and stir to combine. Bring to a boil, then reduce heat low-medium and simmer for about 25-30 minutes, until the potatoes are soft and easily mashable.
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While soup is simmering, prepare crema. Combine sour cream, heavy cream, and salt in a small mixing bowl and whisk until combined. Leave at room temperature until soup is finished.
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Once potatoes are fork-tender, remove thyme sprigs and bay leaf. Use an immersion blender to carefully blend the soup. (Alternatively, you could transfer the soup in small batches to a regular blender and carefully blend it.)
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To prepare croutons, heat broiler to high heat. Place bread slices on a baking sheet and top each slice with one piece of cheese. Transfer tray to the oven and bake for about 2-3 minutes, but keep a close eye on the croutons: each oven is different and you want to take them out before they burn!
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Serve soup with croutons, fresh chives, and dollops of crema.