IEQ has a two-tiered operating structure: (i) an International Advisory Board, consisting of senior scholars who are consulted and relied upon for general guidance and expertise; and (ii) an editorial board consisting of a General Editor, Associate Editors, Assistant Editors, and a Language Editor.

Originally conceived as a project of the Center for Islam and Science (CIS), Canada, IEQ now enjoys the support of universities, academic centers and research institutions around the world. This growing support is indicative of a broadly felt need for such a work.

Established in 2000, the Center for Islam and Science (CIS) is an independent research center dedicated to the promotion of research and diffusion of knowledge on all aspects of Islam, with emphasis on the Islamic intellectual tradition and specifically the Islamic scientific tradition. CIS operates under an international advisory board and a local executive committee. It is a registered not-for-profit organization in the province of Alberta and a registered charity with Revenue Canada. For more details on the work of the Center, please visit its website.

In 2008, the Society for Qur'anic Studies (SQS), Pakistan, was especially formed to collaborate with CIS on this project. It was registered under the Societies Act XXI of 1860, and it functions as an independent research organization with its own board of trustees.