Objective: This article describes the EMPOWER study, a controlled trial aiming to determine the effectiveness and cost-effectiveness of an eHealth intervention to prevent common health problems and reduce presenteeism and absenteeism in the workplace. Intervention: The EMPOWER intervention spans universal, secondary and tertiary prevention and consists of an eHealth platform delivered via a website and a smartphone app designed to guide employees throughout different modules according to their specific profiles. Design: A stepped-wedge cluster randomized trial will be implemented in four countries (Finland, Poland, Spain and UK) with employees from small and medium enterprises (SMEs) and public agencies. Companies will be randomly allocated in one of three groups with different times at which the intervention is implemented. The intervention will last 7 weeks. Employees will answer several questionnaires at baseline, pre- and post-intervention and follow-up. Outcome measures: The main outcome is presenteeism. Secondary outcomes include depression, anxiety, insomnia, stress levels, wellbeing and absenteeism. Analyses will be conducted at the individual level using the intention-to-treat approach and mixed models. Additional analyses will evaluate the intervention effects according to gender, country or type of company. Cost-effectiveness and cost-utility analyses [based on the use of quality-adjusted life-years (QALYS)] will consider a societal, employers’ and employees’ perspective.