Recent developments in the fields of organic synthesis, process research, and biopharmaceuticals are leading to increasingly complex mixtures of closely related species that often prove challenging for analysis, separation, and characterization. Herein, computer-assisted modeling using LC Simulator (ACD/Labs) software is introduced as an initial analytical framework to isolation and purification workflows, enabling the rapid increase of scale-up productivity (kkD: kilograms of purified analyte per kilogram of stationary phase per day) of target pharmaceuticals in multicomponent mixtures. This approach allows us to achieve dramatic increases of kkD while minimizing solvent consumption and hazardous waste by accomplishing three main goals: (1) selectively improving the resolution of only target analytes for the maximum loading while also reducing the cycle time, (2) changing the elution order of the target peaks to prevent coelution caused by undesirable tailing components while increasing sample loading, and (3) enabling the generation of three-dimensional (3D) resolution maps that serve as a database to reduce preparative optimization when similar reaction mixtures are encountered, as typically occurs in the development and manufacturing of new drug substances. Chromatographic simulations served to generate 3D resolution maps with robust separation conditions that matched the outcome of subsequent experimental data (overall relative standard deviation (RSD) of retention times <3% between simulated and experimental conditions). The optimal separation procedures generated through this strategy were successfully applied to the preparative isolation and purification of multicomponent mixtures of closely related species using readily available reversed-phase liquid chromatography (RPLC) and ion-exchange chromatography (IEC) instrumentation, resulting in a substantial increase of purification workflow efficiency in all cases. This computer-assisted modeling approach enables more efficient, cost-effective, and greener preparative chromatography workflows.