AbstractBACKGROUNDNapin and cruciferin, the predominant storage proteins in Brassica napus (rapeseed), exhibit favorable techno‐functional properties such as emulsification and gel formation, positioning them as promising candidates for the encapsulation and delivery of bioactive compounds. Their classification as GRAS (Generally Recognized As Safe), combined with their biodegradability and biocompatibility, highlights their potential as sustainable alternatives to synthetic delivery matrices. However, their broader application is hindered by the absence of scalable purification processes that concurrently ensure high purity and yield.RESULTSThis study presents the development of a fully continuous chromatographic platform for the simultaneous isolation of napin and cruciferin from crude rapeseed extracts. Napin was purified via cation‐exchange chromatography, whereas cruciferin was isolated using anion exchange. Key process parameters were identified through systematic batch screening, with emphasis on the initial binding conditions to enable direct coupling of both chromatographic steps. The optimized protocol permitted efficient sequential protein capture with minimal buffer adjustment, leading to significantly reduced process time and resource consumption. The purified proteins exhibited high purity and are of suitable quality for future applications.CONCLUSIONThe continuous purification process established in this study constitutes a significant step toward the scalable and sustainable processing of plant‐derived proteins. By applying principles of process intensification, the method enhances overall operational efficiency and environmental compatibility. Importantly, the high‐purity napin and cruciferin obtained through this platform provide a promising foundation for future development of bioactive compound encapsulation and delivery systems, supporting the broader integration of plant‐based biopolymers in pharmaceutical and nutraceutical applications. © 2025 The Author(s). Journal of Chemical Technology and Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry (SCI).