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.