Since the implementation of the Excellence Initiative and the Excellence Strategy, German higher education institutions have been restructuring university governance, especially those selected as Universities of Excellence. This study uses a holistic and mission-related integrated governance approach to conduct a qualitative analysis of the governance transformation of German Universities of Excellence, aiming to provoke discussion on transforming governance to optimize organizational effectiveness and sustainable development of German higher education institutions. Transforming governance of German Universities of Excellence involves mission statements, strategic goals, institutional strategies, research, teaching, the third mission, internationalization, global engagement, governance relationships and structures, institutional leadership, funding, autonomy, innovation, digital transformation, quality assurance, and sustainable development, aiming to enhance accountability, performativity, transparency, openness and organizational effectiveness with efficient administrative management in alignment with institutional missions, vision, core values, and strategic goals.