Surface functionalization is found to prevent the reduction of saturation magnetization in magnetite nanoparticles, but the underlying mechanism is still to be clarified. Through a wide set of hybrid density functional theory (HSE06) calculations on FeO nanocubes, we explore the effects of the adsorption of various ligands (containing hydroxyl, carboxylic, phosphonic, catechol, and silanetriol groups), commonly used to anchor surfactants during synthesis or other species during chemical reactions, onto the spin and structural disorder, which contributes to the lowering of the nanoparticle magnetization. The spin-canting is simulated through a spin-flip process at octahedral Fe ions and correlated with the energy separation between O 2p and Fe 3d states. Only multidentate bridging ligands hamper the spin-canting process by establishing additional electronic channels between octahedral Fe ions for an enhanced ferromagnetic superexchange interaction. The presence of anchoring organic acids also interferes with structural disorder, by disfavoring surface reconstruction.