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, and average indirect costs were €9476. In conclusion, no additional benefits were found in effects or cost savings. Therefore, the programme in its current form cannot be recommended for implementation.