This study aims to evaluate the cost-effectiveness of a long-term workplace health promotion programme on physical activity (PA) and nutrition. In total, 924 participants enrolled in a 2-year cluster randomized controlled trial, with departments (n = 74) within companies (n = 6) as the unit of randomization. The intervention was compared with a standard programme consisting of a physical health check with face-to-face advice and personal feedback on a website. The intervention consisted of several additional website functionalities: action-oriented feedback, self-monitoring, possibility to ask questions and monthly e-mail messages. Primary outcomes were meeting the guidelines for PA and fruit and vegetable intake. Secondary outcomes were self-perceived health, obesity, elevated blood pressure, elevated cholesterol level and maximum oxygen uptake. Direct and indirect costs were calculated from a societal perspective, and a process evaluation was performed. Of the 924 participants, 72% participated in the first and 60% in the second follow-up. No statistically significant differences were found on primary and secondary outcomes, nor on costs. Average direct costs per participant over the 2-year period were 376 euros, and average indirect costs were 9476 euros. In conclusion, no additional benefits were found in effects or cost savings. Therefore, the programme in its current form cannot be recommended for implementation. (Contains 4 tables and 1 figures.)