The permanent governance was adopted at the Governing Board meeting, held February 9, 2012 in Paris. 

The governance structure consists of a decision-making Governing Board (GB) and two advisory boards, the Scientific Advisory Board (SAB) and Stakeholder Advisory Board (StAB). These boards are supported by a Secretariat. 

The Governing Board comprises one or two high-level representatives from each of the 24 participating countries that are willing to actively contribute to and participate in JPI operations.

The representatives are typically from research or agriculture ministries, research funding organisations or major research performing organisations that have the authority to take strategic decisions and engage resources from national research funds.