Historically, community engagement (CE) in research has been implemented in the fields of public health, education and agricultural development. In recent years, international discussions on the ethical and practical goals of CE have been extended to human genomic research and biobanking, particularly in the African context. While there is some consensus on the goals and value of CE generally, questions remain about the effectiveness of CE practices and how to evaluate this. Under the auspices of the Human Heredity and Health in Africa Initiative (H3Africa), the H3Africa CE working group organized a workshop in Stellenbosch, South Africa in March 2016 to explore the extent to which communities should be involved in genomic research and biobanking and to examine various methods of evaluating the effectiveness of CE. In this paper, we present the key themes that emerged from the workshop and make a case for the development of a rigorous application, evaluation and learning around approaches for CE that promote a more systematic process of engaging relevant communities. We highlight the key ways in which CE should be embedded into genomic research and biobanking projects.