The aim of this study was to prepare and characterize pectin–silica composites with different surface properties and to evaluate the effect of silica surface modification on pectin immobilization. Unmodified silica (SiO2) and APTES-functionalized silica (SiO2–APTES) were used as inorganic components for the preparation of Pectin/SiO2 and Pectin/SiO2–APTES composites under comparable conditions. The immobilization of pectin was evaluated by viscometric analysis of the residual polymer concentration in the filtrate, while the structural and morphological characteristics of the obtained materials were investigated using Fourier-transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). A pronounced difference in pectin immobilization efficiency was observed for the two silica surfaces. The immobilization efficiency of pectin on unmodified SiO2 was 39.5%, whereas the use of APTES-functionalized silica increased the immobilization efficiency to 98.7%. FTIR analysis confirmed the coexistence of characteristic structural features of silica, APTES-derived organic groups, and pectin in the Pectin/SiO2–APTES composite. Changes in the O–H, carboxyl, and C–H spectral regions indicated interactions between pectin functional groups and the modified silica surface. SEM observations revealed substantial morphological changes after pectin immobilization, with the resulting composite exhibiting a more heterogeneous and densely packed structure compared with the initial silica materials. The obtained results demonstrate that modification of silica surface properties can substantially improve pectin immobilization and influence the structural organization of pectin–silica composites. The prepared materials may be considered promising polymer–inorganic systems for further investigation in adsorption and related surface processes.