Zoombini Isle is the original home of the Zoombinis. They were forced to abandon it after it was taken over by another race, the Bloats. The Bloats had enslaved the Zoombinis for manual labor and built up the island with walls and turrets. (Logical Journey of the Zoombinis)
The Zoombinis then devised a plan to escape from their dominated land. After the Zoombinis put this plan into action, they struggled through many challenges and inhabited their newly known town, Zoombiniville.
As time passed, Zoombini Isle was left desolate as the Bloats no longer had any Zoombinis to rule over, and they no longer had any reason to stay. With that, the Bloats left. Ever since the island was no longer inhabited by the dreaded Bloats, the Zoombinis ventured back to their original home in pursuit of the Snozzleberry fruits and the Zerbles. During that time, others like Arno the pizza troll moved there. (Zoombinis Island Odyssey)