Place the potatoes and butterbeans in a pot and cover with water. Bring to a boil and season the water with salt and pepper; reduce the heat to simmer. Cook until just tender, about 30 minutes. Drain well and set aside.
Heat the oil in a large skillet over medium-high heat. Add the onions and cook until soft and translucent, 3 to 5 minutes. Add the corn and squash and cook, stirring, until crisp-tender, about 5 minutes. Stir in the reserved butterbeans and potatoes. Cook, stirring, until heated through. Add the tomatoes, stirring to combine. Taste and adjust for seasoning with salt and pepper. Serve immediately.