<p>Sporopollenin exine capsules (SECs) are attractive natural microcarriers, but allergenic protein residues remain a critical limitation for biomedical applications. In this study, the development of morphologically restored and deproteinized JSECs from <i>Juglans regia</i> pollen was verified. High-purity capsules were isolated via sequential chemical treatments, followed by a PEG-4000-assisted stabilization process to resolve structural collapse observed during acidolysis. Protein elimination and morphological recovery were validated using SDS-PAGE, solid-state ¹³C CP/MAS NMR, and BET analysis. The absence of detectable protein bands in SDS-PAGE, coupled with attenuation of peptide-associated signals in NMR and FT-IR, indicates that allergenic protein content was reduced below the detection limit of these methods. Morphological analyses revealed that PEG treatment effectively restored the spherical capsule structure, increasing surface area to 13.56 m²/g with a ~ 25% yield. Statistical analysis (<i>n</i> = 150) confirmed an 83.3% morphological recovery rate, demonstrating that PEG-4000 effectively prevents structural collapse while maintaining intact, spherical capsules. These results demonstrate that <i>Juglans</i>-derived capsules can be rendered with high purity while preserving structural integrity, highlighting their potential as sustainable natural carriers for future biomedical applications.</p>