There is a continued need to improve the energy (and by extension carbon) performance of the existing building stock in Europe and globally. Recent experiences with the COVID-19 pandemic have demanded even more of the built environment disciplines when it comes to air quality and ventilation rates particularly in teaching environments which are seen as necessary developmental sectors for the learning of the population. As such it is important that these spaces are safe for students and staff where, until now, infectious disease risk assessments were not typical. In addition to this, there is a risk that envelope refurbishment (which is critical for energy performance) without the provision of adequate ventilation may lead to high-risk scenarios for occupants in university spaces and additional measures may be required. This study presents a design stage risk assessment methodology and applies this to evaluate different retrofitted ventilation approaches combined with additional control measures for a lecture room environment. A real case study lecture room in Ireland was used to demonstrate the methodology for evaluating the airborne infectious disease risk (using the Wells-Riley model) under different ventilation approaches (natural and mechanical), infiltration rates (existing and upgraded), class sizes and times, mask efficiencies as well as the use of an air cleaner. The methodology that was adopted was shown to be flexible and capable of considering a wide range of different retrofit and user specific combinations. The results from the evaluation indicate a wide range in event specific reproductive numbers, however, the use of a well-designed natural or mechanical ventilation system was seen as significant in stabilising or suppressing virus transmission and reducing the likelihood of highly reproductive events. It was found that combinations of measures with ventilation were the most effective at suppressing reproductive numbers. It is recommended that during known pandemics (in the short-term) infectious control strategies should use filtration (through masks or air cleaners) and adequate ventilation. Long-term refurbishment strategies should consider the provision of hybrid ventilation systems which integrate key energy saving measures (such as heat recovery and demand-controlled ventilation), virus control (such as HEPA filtration) and low energy cooling solutions (such as passive cooling).