Abstract Background Healthy lifestyles play an important role in the prevention of premature death, chronic diseases, productivity loss and other social and economic concerns. However, workplace interventions to address issues of fitness and nutrition which include work-related outcomes are complex and thus challenging to implement and appropriately measure the effectiveness of. This systematic review investigated the impact of workplace nutrition and physical activity interventions, which include components aimed at workplace’s physical environment and organizational structure, on employees’ productivity, work performance and workability. Methods A systematic review that included randomized controlled trials and or non-randomized controlled studies was conducted. Medline, EMBASE.com, Cochrane Library and Scopus were searched until September 2016. Productivity, absenteeism, presenteeism, work performance and workability were the primary outcomes of our interest, while sedentary behavior and changes in other health-related behaviors were considered as secondary outcomes. Two reviewers independently screened abstracts and full-texts for study eligibility, extracted the data and performed a quality assessment using the Cochrane Collaboration Risk-of-Bias Tool for randomized trials and the Risk-of-Bias in non-randomized studies of interventions. Findings were narratively synthesized. Results Thirty-nine randomized control trials and non-randomized controlled studies were included. Nearly 28% of the included studies were of high quality, while 56% were of medium quality. The studies covered a broad range of multi-level and environmental-level interventions. Fourteen workplace nutrition and physical activity intervention studies yielded statistically significant changes on absenteeism (n = 7), work performance (n = 2), workability (n = 3), productivity (n = 1) and on both workability and productivity (n = 1). Two studies showed effects on absenteeism only between subgroups. Conclusions The scientific evidence shows that it is possible to influence work-related outcomes, especially absenteeism, positively through health promotion efforts that include components aimed at the workplace’s physical work environment and organizational structure. In order to draw further conclusions regarding work-related outcomes in controlled high-quality studies, long-term follow-up using objective outcomes and/or quality assured questionnaires are required. Trial registration Registration number: PROSPERO CRD42017081837.