Abstract Background Previous research on employee well-being for those who have experienced social and economic disadvantage and those with previous or existing mental health conditions has focused mainly on programmatic interventions. The purpose of this research was to examine how organisational structures and processes (such as policies and culture) influence well-being of employees from these types of backgrounds. Methods A case study ethnographic approach which included in-depth qualitative analysis of 93 semi-structured interviews of employees, staff, and managers, together with participant observation of four social enterprises employing young people. Results The data revealed that young people were provided a combination of training, varied work tasks, psychosocial support, and encouragement to cultivate relationships among peers and management staff. This was enabled through the following elements: structure and space; funding, finance and industry orientation; organisational culture; policy and process; and fostering local service networks.. The findings further illustrate how organisational structures at these workplaces promoted an inclusive workplace environment in which participants self-reported a decrease in anxiety and depression, increased self-esteem, increased self-confidence and increased physical activity. Conclusions Replicating these types of organisational structures, processes, and culture requires consideration of complex systems perspectives on implementation fidelity which has implications for policy, practice and future research.