Nowadays, numerous researches are being performed to formulate nontoxic multifunctional magnetic materials possessing both high colloidal stability and magnetization, but there is a demand in the prediction of chemical and colloidal stability in water solutions. Herein, a series of silica-coated magnetite nanoparticles (MNPs) has been synthesized via the sol-gel method with and without establishing an inert atmosphere, and then it was tested in terms of humic acids (HA) loading applied as a multifunctional coating agent. The influence of ambient conditions on the microstructure, colloidal stability and HA loading of different silica-coated MNPs has been established. The XRD patterns show that the content of stoichiometric Fe₃O₄ decreases from 78.8% to 42.4% at inert and ambient atmosphere synthesis, respectively. The most striking observation was the shift of the MNPs isoelectric point from pH ~7 to 3, with an increasing HA reaching up to the reversal of the zeta potential sign as it was covered completely by HA molecules. The zeta potential data of MNPs can be used to predict the loading capacity for HA polyanions. The data help to understand the way for materials’ development with the complexation ability of humic acids and with the insolubility of silica gel to pave the way to develop a novel, efficient and magnetically separable adsorbent for contaminant removal.