BIHE is an independent and self-governing institution that comprises five faculties and fourteen departments, as well as many offices and associations. Over almost four decades, in response to the demands and requirements it was subjected to, BIHE organizational structure has evolved organically into a resilient governance system of councils and committees, supported by professional services that provide administrative and non-academic assistance.

BIHE seeks steady growth and continuous improvement through a method of action and reflection followed by refinement or correction of approaches officially adopted at all levels and in all of its bodies. To achieve this, BIHE operates in learning mode and cultivates a culture of unceasing learning and improvement. Consultation is one of the core operating principles that enables action-reflection cycles to utilize the diversity and wisdom of all stakeholders to achieve clarity and befitting decisions. Moreover, consultation in an atmosphere of care and mutual respect helps all to develop an understanding and sense of ownership of BIHE and to direct their efforts towards its progress and development. Commitment to justice and special care for the underprivileged are among the other core values and operational principles in BIHE's organization.

Although many of BIHE's staff and academics serve on a voluntary basis, they still provide a rigorous and professional service in a structured, sustainable, and methodical manner.