In global health research and genomics research specifically, community engagement has gained prominence in enhancing ethical conduct, particularly in managing the risk of stigmatization, but there is minimal scientific evidence on how to do this effectively. This article reports on community engagement evaluation strategies in two African genomics studies: the Stigma in African Genomics Research study and the Genomics of Schizophrenia in South African Xhosa People (SAX) study. Within the Stigma in African Genomics Research study, a self-report rating scale and open-ended questions were used to track participant responses to an experiential theatre workshop. The workshop focused on participant experiences of living with schizophrenia or rheumatic heart disease (RHD). While the schizophrenia group reported more alienation and less stigma resistance than the RHD group, both groups demonstrated increased stigma resistance over time, after participating in the workshops. Hearing from others living with and managing the same illness normalised participants’ own experiences and encouraged them. Within the SAX study, a short rating scale and qualitative feedback methods were used to evaluate a Mental Health Literacy Day targeting mental health stigma. Information talks about (i) the symptoms of schizophrenia and treatment options and (ii) the illness experiences of a patient in recovery were rated as the most helpful on the day. Audience members reported that these talks challenged negative perceptions about severe mental illness. Three important learnings emerged from these evaluations: firstly, integration of evaluation strategies at the research study planning phase is likely to promote more effective community engagement. Secondly, a combination of quantitative and qualitative methods that draw on simple descriptive statistics and thematic analysis can provide nuanced perspectives about the value of community engagement. Thirdly, such evidence is necessary in establishing and promoting the science of community engagement in genomics research and health research more broadly.