Shift work is known to be associated with poor health outcomes, however our understanding of health behaviours (sleep, physical activity and nutritional intake) longitudinally in shift workers is currently limited. Systematic searches of four data bases were conducted. Using PRISMA-ScR guidelines we report a scoping review of 15 eligible studies. Of the included studies, 11 studies examined sleep outcomes, three examined physical activity and two examined nutritional intake. The number of follow ups conducted in each study varied from one to six, with the majority of studies reporting one follow up. Study length varied from six months to 16 years. Findings suggest that shift workers have stable but largely insufficient sleep longitudinally. Many shift workers, particularly inexperienced shift workers, are additionally experiencing poor sleep quality. There is limited data longitudinally on physical inactivity and nutrition intake, but included studies indicate that shift workers may also be physical inactive and with some poor nutritional intake (i.e., high levels of saturated fat intake). Longitudinal studies of shift work with multiple follow-ups are needed to address the current gaps in literature. The evidence that shift workers may be susceptible to poor health behaviours longitudinally is important as it provides a means by which strategies and interventions can be targeted, at both individual and organisational levels, to assist in better long term health outcomes.