Biological organisms possess an unparalleled ability to control crystallization of biominerals with convoluted internal structures. For example, an occluded organic matrix can interact with the mineral during its formation to control its morphology and structure. Although related matrix proteins that preferentially nucleate minerals have been identified, the mechanisms elucidating the structural and chemical complexity of calcium oxalate biominerals in plants remain unclear. Here, we show that a protein nanofiber (14 kDa) is embedded inside raphide (needle-shaped calcium oxalate) crystals of banana (Musa spp.), and that nanometer-scaled calcium oxalate spheres are arranged along the long axes of this central proteinaceous filament to form laminated structures through an aggregation-based growth mechanism, resulting in the final product of elongated and tapered hexagonal crystals. We further demonstrate that 11 amino acid peptide segments, with hydrophilic and hydrophobic residues rich in proline derived from the C-terminus of this full protein sequence, in vitro self-assemble into fibers and accelerate calcium oxalate nucleation kinetics. Remarkably, elongated and organized microstructures which are similar in appearance to natural raphide crystals are formed, emphasizing interactions between the mineral and self-assembled protein fibers. We anticipate that the present investigation of the structural and morphological complexity of plant calcium oxalate crystals and the underlying mechanisms of their formation will contribute to our understanding not only how plants evolved these sophisticated structures and morphologies for survival and adaptation, but also ultimately provide useful clues about how to maximally sequester calcium ions and/or oxalate in a confined compartment.