To date, little research has been conducted on subject leadership by primary and/or junior secondary school heads of department (HODs). Unlike their senior secondary school counterparts, South African science HODs have the more complex task of leading in the multidisciplinary context of natural sciences (NS1). Such leadership comes in addition to the complications of role ambiguity, limited time and authority that are inherent in the HOD position. Using interviews and 360° multi-rater by four teachers and subject meeting observations, data were transcribed and categorised into themes that describe the instructional leadership practices of three NS HODs in South Africa. This paper is part of a more comprehensive PhD study. It suggests that providing leadership for NS teaching is more complex in practice than has been reported to date. In the context of increasing focus on accountability and national testing, the unintended consequence has been the neglect of the junior secondary NS teachers by the HODs. Furthermore, the data suggest that the HODs tend to limit their attention to areas of their own specialisation. The paper concludes with a conceptual framework that provides guidance for improving instructional leadership by the HODs in such multidisciplinary contexts, especially for the junior secondary school levels. It also recommends the restructuring of the conglomerate departments to make them more effective.