The main bottleneck for the industrial implementation of highly promising multi-phase whole-cell biocatalytic processes is the formation of stable Pickering-type emulsions, hindering efficient downstream processing. Especially for the crucial step of phase separation, state-of-the-art processes require time-consuming and costly process steps (excessive centrifugation/use of de-emulsifiers). In contrast, using the phenomenon of catastrophic phase inversion (CPI), efficient phase separation can be achieved by addition of an excess dispersed phase within minutes. To show applicability of CPI as an innovative process step, a fully automated lab-scale prototype was designed and constructed within this work. A simple mixer-settler set-up enabled a continuous phase separation using CPI termed applied catastrophic phase inversion (ACPI). Test runs were conducted using emulsions from biphasic whole-cell biocatalysis (Escherichia coli JM101 and Pseudomonas putida KT2440 cells). Solvents used included n-heptane, ethyl oleate or 1-octanol as organic phase. These investigations revealed ideal process settings for a stable ACPI process (e.g., flow/stirring rates and volumetric phase ratios between organic and water phase). The knowledge of the CPI point is most crucial, as only the inverted state of emulsion is successfully destabilized.