Fill a large saucepan 3/4 full with water and bring to a boil. Add the lima beans and cook until just tender-crisp, about 6 minutes. Transfer with a slotted spoon to a bowl of ice water to stop the cooking. Drain and set aside.
In a saucepan, heat 1 tablespoon of the olive oil over medium heat. Add the tomato, onion, garlic, bay leaf, thyme and salt. Saute until the vegetables soften, about 5 minutes.
Add the stock and bring to a boil over medium-high heat. Reduce the heat to low, add the cooked lima beans and simmer, uncovered, until heated through, 2 to 3 minutes. Discard the bay leaf and transfer to a serving bowl. Drizzle with the remaining 1 tablespoon olive oil and sprinkle with the chopped parsley.