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Step 1
For the soup: In a large bowl, combine the cannellini beans, chickpeas and navy beans and add enough water to cover by several inches. Soak for 8 hours or overnight in the refrigerator. Drain and rinse.
Step 2
Heat the olive oil in a large Dutch oven over medium heat. When the oil is hot, add the carrots, celery and leeks. Season with a couple good pinches of salt and cook, stirring occasionally, until the leeks are softened but not browned, 5 to 6 minutes. Add the garlic, rosemary, thyme and red pepper flakes and cook until sizzling and fragrant, about 1 minute. Add the broth, water, drained beans, bay leaves, lemon peel and Parmesan cheese rind. Bring to a boil and reduce to a simmer. Cook, uncovered, until all 3 beans are tender and the soup is slightly thickened, about 2 hours, or longer, if needed.
Step 3
Once the beans are tender, taste the broth and season with more salt, if needed. Add the kale and simmer until tender, about 10 minutes more. Remove and discard the bay leaves, lemon peel and what’s left of the Parmesan rind.
Step 4
Meanwhile, make the challah croutons.
Step 5
For the challah croutons: Arrange an oven rack in both the middle and upper positions. Preheat the oven to 400 degrees F. Line a baking sheet with parchment paper.
Step 6
Add the sliced challah to the prepared baking sheet. Bake in the oven on the middle rack until lightly toasted, flipping once, about 5 minutes. Remove from the oven and brush the tops with the melted butter and switch the oven to broil. In a small bowl, add the Gruyère and Parmesan cheeses and toss to combine. Cover the tops of the challah slices completely with cheese. Broil on the top rack until browned and bubbly, 1 to 2 minutes depending on the strength of your broiler.
Step 7
Ladle the soup into bowls, with a drizzle of olive oil if desired, some flaky salt and freshly ground black pepper. Top each serving with a challah crouton.
Step 8
Leftover soup will keep in the refrigerator for at least 3 to 4 days, though you may want to add a little water when reheating as it will thicken over time. It also freezes well for up to 3 months.