The organisational structure of MaYA is that of a registered Purpose Foundation. The scope of the Foundation is to have a holistic overview of the whole agricultural sector in the Maltese Islands; from production to consumption, and with a broad view of the economic, environmental and social impacts.

Unlike many other organisations where specific individual members' interests are represented under one name, the Foundation aims to gather its insight from a vast spectrum of Supporters who are not directly benefiting personally from the affiliation and work carried out. However, by means of this giving approach, the different segments which make up the islands' agriculture sector, and their different stakeholders, are supported through a bottom-up approach. This is done without bias towards specific sectors or individuals and allows for apolitical, independent and autonomous actions.