ILTER places emphasis on solid and professional internal structures which provide the institutional framework for its long-term operations in line with its strategic goals. Through its governance structures, ILTER is accountable towards its members, responsibilities can clearly be defined and distributed among the network's officers, transparency is given regarding ILTER's actions, its collaborations with other networks and organizations, and regarding how its funds are spent.

Fairness is ensured by defining clear mechanisms for all the members to get involved in decision making. Such good management practices are essential for networks and research infrastructures with a long-term perspective. Specific activities and progress often rely on temporary funding sources, such as international research projects, but beyond these, well-functioning operational structures and related governance ensure continuity.

ILTER is a network of networks. Most of its members are national LTER networks, consisting of scientists collectively engaged to conduct scientific research according to the ILTER mission, vision and goals. Each of these networks has its own long-term program and has become part of the ILTER legal entity. Some of the ILTER member networks are structured into ILTER Regional Groups: LTER Europe and ILTER East Asia Pacific (EAP).

The ILTER Chair convenes and presides at the Coordinating Committee meetings and Executive Committee meetings, and ensures that the business of ILTER is carried out effectively and in accordance with its committee's decisions. The Co-Chair supports the Chair and takes over the Chair’s role in case the Chair is absent.

The IMO provides day-to-day support for the ILTER chair's work and administers the ILTER action items. It provides support regarding ILTER meetings, including minute taking, set up of virtual meeting tools etc., and it handles central communication, such as mailing lists and circulars and ILTER correspondence.

The ILTER Secretariat handles the financial administration of the association and of its initiatives. It hosts the document store and the central contacts database. It performs contractual work and legal obligations, is responsible for data security and maintains this website. Both offices closely collaborate.

The ILTER EC is responsible for day-to-day organizational aspects of ILTER in between the ILTER CC meetings. Thereby it puts decisions taken by the ILTER CC into action. The ILTER EC interacts virtually, holding a monthly teleconference. The ILTER EC encompasses the Chair and the Co-Chair, the IMO-Officer (International Management Office) and the Secretary, the chairs of the standing Committees for Science and Information Management, and representatives of US LTER, SAEON (South African Environmental Observation Network), and the regional groups ILTER EAP, and LTER Europe.

ILTER has established two standing committees, namely for Science and for Information management. For specific purposes, also ad hoc committees have been set up, for example to work out guidelines for internal balance.