The General Assembly is a decision-making structure that was made compulsory in all Brazilian public companies by Law on Public Companies (Law 13303, from June 30, 2016, regulated by Decree 8945, from December 27, 2016).

The main goal of this new board is to promote greater clarity and transparency to the decision-making process and precision in the control of state agencies. Said Decree establishes the governance structure of state-owned and state-controlled companies, defining that the General Assembly makes decisions related to the shareholders (that is, to the Federal Government, known as the Union in law); that the Administrative Council (Consad) takes on the role of strategic guidance and liaison between property and management, supervising the Board of Directors; and that the Executive Board is in charge of the company's management.

The General Assembly shall mandatorily take place through an annual ordinary meeting, always in the first quarter of the year, and led by the chairman of Embrapa's Administrative Council (Consad). The meeting's mandatory agenda is the analysis and assessments of the books by Embrapa's administrators and deliberation on the financial records presented.

The Assembly can also extraordinarily gather to play other roles like, for instance, changing the capital stock or Embrapa's social statute, or choose and dismiss members of the corporation's councils at any time.

As it is a public company that relies on the Union's budget, Embrapa has a single shareholder, which is the Union itself. Therefore, the Assembly is composed of a single member that, in accordance with Decree 147/1967, is represented by the Office of the Attorney General of the General Treasury (PGFN). To compose the vote to be cast at the Assembly, PGFN consults two advisory tiers: the Ministry of Economy and the Ministry of Agriculture, Livestock and Food Supply.