Inter-agency partnerships are critical for addressing the interrelated circumstances associated with the social and health determinants of health inequalities. However, there are many challenges in evaluating partnership processes and outcomes. We discuss a mixed methods study that explored partnership processes in an innovative program that aims to promote social and economic inclusion for young newly arrived refugees. A theoretically informed evaluation was designed and data collected in three ways: an organizational ethnographic approach; a partnership self-assessment tool and semi-structured interviews. Partnership assessments and interviews were collected at two points in time providing progressive process data. Analyses explore divergent levels of staff satisfaction with the partnership's operations, particularly between staff working in program development (strategic management) and program delivery (service provision) roles. Follow-up data collection indicated satisfaction with partnership processes had improved. The partnership did achieve its aim of increasing the level of cooperation between service providers to support young people from refugee backgrounds. This paper presents insights into how to evaluate inter-agency partnerships and reports both methodological and empirical findings. It provides an approach for a better understanding of the levels at which individuals operate within such partnerships, indicates areas where support and attention is needed.