The market for products made by biotechnology is diverse and has significantly grown in recent years. Despite this growing demand, the first proposal of product purification processes for these complex mixtures remains purely experimentally based and is not methodically targeted. The present work represents an initial study to demonstrate the benefits of a systematic approach. The study focuses on the adaptation of established methods for process development to these so-called complex mixtures. It also assesses the suitability of these methods for complex mixtures, given the current state of research. Based on the described adaption, the most efficient method for the conceptual process development is identified and is subsequently developed. The resulting methodology consists of model-based cost accounting with a miniaturized experimental determination of model parameters, accompanied by a comprehensive error analysis. The developed approaches are successfully validated by using a protein mixture.