The presented manuscript deals with the impact of manufacturing flexibility on the sustainability justification of the manufacturing system, related to manufacturing sustainable social, environmental and financial impact. Such impact is not described in the research sphere. The complexity of the optimisation parameters is reflected in the multi-objective nature that can be evaluated with the use of the simulation study method. The manuscript presents a description of manufacturing flexibility modelling, with respect to the four-level architectural model, describing an optimisation problem of high-mix low-volume production. The impact of manufacturing flexibility on the sustainability justification is presented by the new block diagram. Sustainability parameters' mathematical modelling is presented with two main optimisation parameters of energy consumption and machine scrap percentage. The impact is evaluated and described by an appropriate multi-criteria optimisation method on a sustainably justified production system.