MreB is a structural membrane-associated protein which is one of the key components of the bacterial cytoskeleton. Although it plays an important role in shape maintenance of rod-like bacteria, the understanding of its mechanism of action is still not fully understood. This study shows how segmented flow and microdroplet technology can be used as a new tool for biological in vitro investigation of this protein. In this paper, we demonstrate cell-free expression in a single emulsion system to express red fluorescence protein (RFP) and MreB linked RFP (MreB–RFP). We follow the aggregation and localisation of the fusion protein MreB–RFP in this artificial cell-like environment. The expression of MreB–RFP in single emulsion droplets leads to the formation of micrometer-scale protein patches distributed at the water/oil interface.