Abstract Background Prolonged sitting, a significant risk factor for increased morbidity and mortality, is accumulated mostly in the workplace. There is limited research targeting specific at-risk populations to reduce occupational sedentary behaviour. A recent study found that professional males have the longest workplace sitting times. Current evidence supports the use of multi-level interventions developed using participative approaches. This study’s primary aims are to test the viability of a future definitive intervention trial using a randomised pilot study, with secondary aims to explore the acceptability and feasibility of a multicomponent intervention to reduce workplace sitting. Methods Two professional companies in Dublin, Ireland, will take part in a cluster randomised crossover pilot study. Office-based males will be recruited and randomised to the control or the intervention arms. The components of the intervention target multiple levels of influence including individual determinants (via mHealth technology to support behaviour change techniques), the physical work environment (via provision of an under-desk pedal machine), and the organisational structures and culture (via management consultation and recruitment to the study). The outcomes measured are recruitment and retention, minutes spent sedentary, and physical activity behaviours, work engagement, and acceptability and feasibility of the workplace intervention. Discussion This study will establish the acceptability and feasibility of a workplace intervention which aims to reduce workplace SB and increase PA. It will identify key methodological and implementation issues that need to be addressed prior to assessing the effectiveness of this intervention in a definitive cluster randomised controlled trial.