In vitro precipitation assays are often applied to support drug and formulation development. Current methods applied to quantify the amount of dissolved drug, in particular (U)HPLC, require time-consuming sample preparation. Furthermore, small precipitates formed during the nucleation phase may not be removed quantitatively by filtration or centrifugation of the sample. Given the drawbacks of standard (U)HPLC analyses during the application in transfer experiments, it was the aim of this work to develop a robust and simple to implement in-line UV spectrophotometric method which accurately reflects the precipitation profile obtained from in vitro transfer assays. Based on the three model compounds cinnarizine, dipyridamole, and ketoconazole, the manuscript describes the development of a design of experiments (DoE) based approach to develop derivative UV spectrophotometric methods accounting for the change in media composition over time due to the dilution of simulated intestinal with simulated gastric fluid. An R script was developed which automatically identifies suitable wavelengths for in-line measurements. As an outcome of this study, a fast, robust, accurate, and specific derivative UV spectrophotometric methodology for measuring the concentration of dissolved drugs in in vitro transfer experiments was successfully developed. This method can flexibly be applied to multi-compartmental precipitation assays.