Sekolah Nusa Alam is a non-profit institution, established under Indonesian law and governed by a legally-constituted foundation, called Yayasan Nusa Alam. In line with Indonesian law, the Yayasan consists of three bodies:
- The Board of Trustees (BOT or Badan Pembina)
- The Board of Supervisors (BOS or Badan Pengawas)
- The Board of Management (BOM or Badan Pengurus)