Previous international literature describes a lack of systematic research about cross-institutional cooperation in social and health services although the need is indicated. More and more children and adolescents have complex psychosocial needs. Thus, they require help from different institutions and professions to receive optimal care. However, there is a great need of improvement of the cooperation between institutions in social (e.g. Youth Welfare Office) and health services (e.g. Child and Adolescent Psychiatry (CAP), even in Germany. Therefore, an official Agreement of Cooperation (AoC) between these institutions was implemented as a first attempt to enhance and structure cross-institutional work in Dresden, Germany. This methodological paper describes the corresponding evaluation project that includes cross-sectional and longitudinal assessments. It thereby focuses on the employees' and families' satisfaction as well as the psychosocial development and mental health of children at the intersection of the aforementioned institutions before and after the implementation of the AoC. In addition, it gives a review of literature about cross-institutional work.