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Understanding the plant cell wall architecture is essential for elucidating its biological function and mechanical properties. This study employs a synthetic approach using spherical core–shell capsules with shells composed of deuterated bacterial cellulose (d-BC) and pectin. The shell structure was created via a bottom-up layer-by-layer assembly onto CaCO3 templates, followed by characterization through microscopy and scattering techniques. Small-angle X-ray scattering (SAXS) and confocal laser scanning microscopy revealed increased pore sizes in hydrated d-BC/pectin shells compared to those of hydrated wood-derived cellulose nanofiber (CNF)-based shells from a previous study. Using small-angle neutron scattering (SANS) with contrast variation, structural changes of individual wall components under varying salinities (0 or 10 mM NaCl) were analyzed. The presence of NaCl selectively influenced the pectin phase, while the d-BC network retained structural stability, highlighting its robustness as a wall component. This platform provides a useful tool for testing hypotheses and advancing our understanding of cell wall porosity and composition-dependent permeability.