The possibility of application of chitosan-modified zeolite as sorbent for Cu(II), Zn(II), Mn(II), and Fe(III) ions and their mixtures in the presence of N-(1,2-dicarboxyethyl)-D,L-aspartic acid, IDHA) under different experimental conditions were investigated. Chitosan-modified zeolite belongs to the group of biodegradable complexing agents used in fertilizer production. NaP1CS as a carrier forms a barrier to the spontaneous release of the fertilizer into soil. The obtained materials were characterized by Fourier transform infrared spectroscopy (FTIR); surface area determination (ASAP); scanning electron microscopy (SEM-EDS); X-ray fluorescence (XRF); X-ray diffraction (XRD); and carbon, hydrogen, and nitrogen (CHN), as well as thermogravimetric (TGA) methods. The concentrations of Cu(II), Zn(II), Mn(II), and Fe(III) complexes with IDHA varied from 5–20 mg/dm3 for Cu(II), 10–40 mg/dm3 for Fe(III), 20–80 mg/dm3 for Mn(II), and 10–40 mg/dm3 for Zn(II), respectively; pH value (3–6), time (1–120 min), and temperature (293–333 K) on the sorption efficiency were tested. The Langmuir, Freundlich, Dubinin–Radushkevich, and Temkin adsorption models were applied to describe experimental data. The pH 5 proved to be appropriate for adsorption. The pseudo-second order and Langmuir models were consistent with the experimental data. The thermodynamic parameters indicate that adsorption is spontaneous and endothermic. The highest desorption percentage was achieved using the HCl solution, therefore, proving that method can be used to design slow-release fertilizers.