The whole-cell nitrilase-catalyzed asymmetric hydrolysis of nitriles is a green and efficient preparation approach for chiral carboxylic acids, but often suffers from toxicity and cell lysis from organic substrates. In this work, a novel integrated process for whole-cell nitrilase-catalyzed asymmetric hydrolysis was developed for the first time by introducing a biocompatible ionic liquid (IL)-based biphasic system. The whole-cell nitrilases displayed an outstanding stability and recyclability in the biphasic system and still retained > 85% activity even after 7 cycles reaction. A preparative-scale fed-batch hydrolysis of o-chloromandelonitrile to (R)-o-chloromandelic acid (R-CMA) was performed using the integrated process. The results revealed a yield of 91.3% and a space–time yield of 746.4 g·L⁻¹·d⁻¹, which are currently the highest reported values for R-CMA biosynthesis. The proposed integrated process avoids substrate inhibition, facilitates the reusability of whole-cell nitrilases, and thus shows great potential for the sustainable production of chiral carboxylic acids.