Originally, the centre's name was the Malindo Nusantara Research Centre. The institution encountered a period of stagnation, impeded by multifaceted challenges. In a strategic rebranding, it was renamed the International Nusantara Research Centre Jogyakarta, or I-Nusa Jogja, symbolising a rejuvenated fervour. This transformation harbours the aspiration that the centre will burgeon, furthering its invaluable contributions to the residents of Nusantara.

Over the years, the institution has broadened its horizons, forging ties with international partners and boasting an extensive network with various esteemed institutions, which has been instrumental in its development and outreach.