A global movement towards the creation of “green” buildings is currently underway. Although driven primarily by an external environmental agenda such as energy or carbon, there is growing recognition that greener buildings could affect the Indoor Environment Quality (IEQ). However, localised green building codes, especially in the developing world, often do not systematically recognise IEQ or health as crucial issues, which therefore remain understudied. Since the developing world alone is expected to nearly double current global built floor space by 2050, it is crucial that green buildings perform holistically to be effective. Here, we follow 120 employees of a single organisation as they transition from four conventional office buildings to the first green building (GB), designed to the local Jordanian Green Building Guide. We ask if the move has a positive effect on occupant perception of IEQ, thermal comfort and prevalence of Sick Building Syndrome (SBS), using a repeated-measures protocol. Statistically significant differences in thermal conditions, positively biased towards the GB, were observed across the move, and this enhanced occupant thermal comfort. Surprisingly, no significant improvement in occupant perception of air quality, visual and acoustic comfort was detected after moving to the GB, while odour, mental concentration, and glare were perceived to be poor in the GB and associated with an increase in the prevalence of SBS symptoms. Hence, our results support the growing concern that green buildings may create unintended consequences in terms of occupant comfort and health in the pursuit of a better thermal environment and energy efficiency.