In the pharma and fine chemical industries, the development of continuous flow technologies is a process intensification step of primary importance towards the manufacturing of high-quality products, while reducing the environmental impact and cost of production. The sustainability and profitability of a process can be measured through life cycle Assessment and cost evaluation. However, when applied to emerging technologies, these need to be performed at different stages of the process development in order to limit the uncertainties arising from the scale-up, and hence providing high-fidelity projections of environmental impacts and costs at larger scales. The output of the assessment can in fact vary significantly depending on the maturity of the technology and this translates into having different results at commercial scale compared to early estimations. Therefore, in this article, we perform an assessment at two different scales of production, lab and mini-pilot scale, with the aim of quantifying the uncertainties of the assessment related to the scale-up, identifying the hotspots of the system, and hence providing guidelines for the further steps of process development. The subject of the assessment is the continuous flow synthesis of Rufinamide. It is the first time that this synthesis is evaluated at pilot-scale. The results show that low yields in the cycloaddition drastically affect the waste management and the production of precursors, and hence increases environmental impacts and cost of production. This calls for the need of prioritizing the optimization of this synthesis step in order to deploy a green and economically competitive production technology.European Union's Horizon 2020 research and innovation, Grant/Award Number: Marie Sklodowska-Curie grant agreement no.721290