Trimming of β-(1,3) and β-(1,6)-galactosyl residues from type II arabinogalactan side chains causes an increase in the methyl esterification degree of homogalacturonan in Arabidopsis seed coat mucilage. Arabinogalactan proteins (AGPs) are involved in various physiological processes, such as cell elongation, xylem differentiation, resistance to abiotic stresses or secretion and adherence of seed coat mucilage, a structure suggested as a model system for cell wall studies. The specific roles of AGPs are not fully established, although their carbohydrate motif (type II arabinogalactan, AGII) seems to be essential, being able to mediate interactions with different signalling molecules or with other cell wall polysaccharides. The aim of the present work is to determine the role of AGII from AGPs in the structural organization of the cell wall, using Arabidopsis thaliana plants that overproduce β-galactosidase βV-Gal from Cicer arietinum (35S::βV-Gal plants), an enzyme that acts specifically on the β-(1,3) and β-(1,6)-galactosyl bonds of AGII. The characterization of the seed coat mucilage has allowed us to establish a cell wall homeostasis mechanism in which the neutral side chains of the AGII of the AGPs determine the degree of HG methyl esterification. Thus, the reduction in the galactose is accompanied by an increase in the level of esterification, probably as a compensatory mechanism to maintain the mechanical properties of this specialized cell wall and its hydration properties.