The strive toward sustainability increases the demand for bio‐based material production, forcing expansion of the biorefinery feedstock supply from forest wood to non‐woody materials such as agricultural residues. As a model organism for legume crops, the aptness of agricultural lupins as a lignocellulose feedstock is investigated. Principle chemical analysis combined with optotracing, in which the fluorescent tracer molecule Carbotrace 680 generates a visual map of the native tissues’ lignocellulose anatomy at sub‐cellular resolution, enables informed design of a mild recovery process. A streamlined conversion approach is then designed, yielding lignin‐containing microfibrillated cellulose. By monitoring defibrillation and delignification throughout the extraction process, the use of optotracing for non‐destructive fiber analytics at unprecedented details across all hierarchical structures of lignocellulosic materials is demonstrated. This crop valorization is a prime illustration of a holistic use of lupin biomass, with seeds serving as plant‐based food sources, and other parts as sources for lignocellulose‐based materials, thereby expanding both the biorefinery concept and feedstock supply.