Preheat oven to 375°F. Peel beets, onion, potatoes, and carrots and cut into 1 1⁄2-inch cubes. Add vegetables to a sheet pan, toss with olive oil, salt, and pepper. Bake until vegetables are tender, about 40–45 minutes. Remove and let cool.
In a large pot over medium heat, add stock, roasted vegetables, bay leaves, and garlic. Bring to a boil, cover, and reduce heat to a simmer, and cook for about 15 more minutes. Remove the bay leaves. Transfer to a blender and blend until smooth.
Ladle soup into serving bowls and finish with a grating of fresh nutmeg, a dollop of crème fraîche, a drizzle of olive oil, chive blossoms, and flowers.