Abstract Background In the current labour system many workers are still exposed to heavy physical demands during their job. In contrast to leisure time physical activity (LTPA), occupational physical activity (OPA) is associated with an increased risk of cardiovascular diseases and all-cause mortality, termed “the physical activity (PA) health paradox”. In order to gain more insight into the PA health paradox, an exploration of structural preventive measures at the workplace is needed and therefore objective field measurements are highly recommended. The objective of this paper is to provide an overview of the protocol of the Flemish Employees’ Physical Activity (FEPA) study, including objective measurements of PA, heart rate (HR) and cardiorespiratory fitness (CRF) to gain more insight into the PA health paradox. Methods A total of 401 workers participated in the FEPA study across seven companies in the service and production sector in Belgium. The participants comprised 167 men and 234 women, aged 20 to 65 years. OPA and LTPA were assessed by two Axivity AX3 accelerometers on the thigh and upper back. Ambulatory HR was measured by the Faros eMotion 90° monitor. Both devices were worn during two to four consecutive working days. In addition, CRF was estimated by using the Harvard Step Test. Statistical analyses will be performed using Pearson correlation, and multiple regression adjusted for possible confounders. Discussion This study aims to provide a better insight in the PA health paradox and the possible buffering factors by using valid and objective measurements of PA and HR (both during LTPA and OPA) over multiple working days. The results of the study can contribute to the prevention of cardiovascular disease by providing tailored recommendations for participants with high levels of OPA and by disseminating the results and recommendations to workplaces, policy makers and occupational health practitioners.