According to the Millennium Challenge Compact Agreement, the Government of Indonesia is required to form a Millennium Challenge Account (MCA) as the institution that will manage the grant. On 2 April 2013, MCA-Indonesia then officially came into being as the Institutional Trustee of the Compact Grant, based on the Regulation of the Minister of National Development Planning /Head of the National Development Planning Agency Number 2/2012 (Peraturan Menteri Negara Perencanaan Pembangunan Nasional/Kepala Badan Perencanaan Nasional Nomor 2 Tahun 2012). Since then, the Compact Program has officially operated in Indonesia.

The diagram below shows the structure of the Compact management structure, following the Implementing By law Regulations of Trustee Institution of MCA-Indonesia.