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Step 1
Preheat the oven to 450°F (232°C).
Step 2
In a large bowl, toss the tomatoes with 1/4 cup of the olive oil, the vinegar, garlic, 2 teaspoons of the salt, and the black pepper. Transfer the tomato mixture (including all of its liquid) to a large, heavy rimmed baking sheet. Arrange the tomatoes in a single layer, skin side down. Roast until the tomatoes are charred on the edges, about 40 minutes. Let cool slightly. Slip the skins off the tomatoes.
Step 3
Meanwhile, heat the remaining 2 tablespoons olive oil in a heavy pot over medium heat. Add the onions and the remaining 1 teaspoon salt and cook, stirring often, until the onions are quite soft, about 10 minutes. Add the basil, parsley, and sage and sauté for about 1 minute.
Step 4
Stir in the roasted tomatoes and garlic along with all the accumulated juices from the baking sheet and bring to a simmer. Add the water and simmer gently just until the flavors meld, about 8 minutes. If a smoother consistency is desired, blend all or a portion of the soup with an immersion or standing blender.
Step 5
While the soup simmers, reduce the oven temperature to 375°F (190°C). Toss the bread cubes, basil, dill, rosemary, black pepper, and salt in a medium bowl. Drizzle the oil over the herbed bread cubes and toss to coat. Arrange the bread cubes in a single layer on a rimmed baking sheet. Bake until the croutons are golden brown, stirring occasionally to ensure even browning, about 15 minutes. Let cool.
Step 6
To serve, ladle the soup into bowls, garnish with some of the croutons, if you please, and serve. (This soup is best eaten the day it is made, but it can be covered and refrigerated for up to 1 day. To rewarm, bring the soup to a simmer over medium heat, stirring occasionally and adding water to thin the soup to the desired consistency.)