Extraction is a downstream process option in biobased processes. Because knowledge of phase‐separation behavior is essential for designing efficient separation processes, this study investigates the settling and coalescence behavior of biobased extraction systems by using a standard laboratory‐scale settling cell. The influence of different buffer media and Escherichia coli cells on coalescence was determined for the reactive extraction of hexane‐1,6‐diamine with isostearic acid and di(2‐ethylhexyl)phosphoric acid by using kerosene and oleyl alcohol as diluents. As a result, an increasing pH value of the buffer significantly increases the settling time. The presence of E. coli cells hinders phase separation of the investigated systems, in particular, with dispersed organic phases.