As a prime contender to revolutionise the global auto industry, automated vehicles deployment in cities and within the transport ecosystem requires further investigation. This has also become a prime concern because of the current Covid-19 situation. The introduction of automated minibuses could cause major modal shifts towards or away from public transport. Thus, it is crucial to predict potential deployments and determine their implications to avoid repeating an individual-centric mobility model. This paper suggests possible future scenarios of automated minibuses deployment and calculates the environmental impact through externalities caused by these modal shifts (from traditional transport to automated minibuses). Based on scenario planning and externalities calculations, a methodology is presented and applied to a case study of Geneva using data from a mobility census of Geneva in 2015 and insights from a European project, AVENUE. First, the analysis presents marginal external costs for the automated minibuses. Then, it describes 3 scenarios that highlight the integration of the automated minibuses in public transport and their effects on modal shares. The assessment shows that replacing all cars with automated minibuses produces the best savings of externalities. Replacing all buses with automated minibuses leads to higher externalities. The integration of the automated minibuses as part of mobility-as-a-service MaaS is the most feasible and scalable. The study emphasises the role of targeted policies to optimise the benefits of automated minibuses.