We investigate how the environment affects the galaxy structure in the Spiderweb protocluster at z = 2.16 using JWST/NIRCam F115W, F182M, and F410M imaging (rest-frame ~3500 Å to 1.4 μm). We performed homogeneous multi-wavelength parametric modelling of the single-Sérsic and bulge--disc decomposition for a sample of 103 Spiderweb member galaxies within the JWST field of view (up to ~2 × R200). Star-forming galaxies (SFGs) follow a mass-size relation broadly consistent with the field, with a mildly steeper trend at the high-mass end, within uncertainties. Passive galaxies exhibit a flatter mass--size relation, and their typical size (intercept at fixed stellar mass) lies between that of the coeval field and cluster passive populations, indicating an intermediate evolutionary stage. In both star-forming and passive systems, bulges are systematically more compact than discs. Galaxy sizes decrease slightly with increasing wavelength, whereas ALMA-detected dusty SFGs exhibit a much steeper wavelength dependence, consistent with centrally concentrated, obscured star formation. The passive fraction depends primarily on local density: it resembles the field at Σ ≲ 100-200 gal Mpc-2 and rises to ~60% at Σ ≳ 1000 gal Mpc-2; however, the uncertainties are relatively large due to the small number of galaxies in the highest-density bins, and we find no significant additional dependence on clustercentric distance. We also find a weak but significant correlation between local density and Sérsic index (strongest in F410M), but no clear correlation with effective radius or the star formation rate surface density ΣSFR. These results support a picture in which quenching and structural transformation are already advanced, while size growth is still ongoing.