This study focuses on the fabrication of a novel sensing platform on a screen-printed carbon electrode, modified by a combination of hydrothermally synthesized iron dioxide (ε-Fe2O3) nanoparticles and Chitosan (CS) biopolymer. This unique organic-inorganic hybrid material was developed for Electrochemical Impedance Spectroscopy (EIS) sensing, specifically targeting heavy metal ions that include Hg2+, Cd2+, as well as Pb2+. The investigation encompassed a comprehensive analysis of various aspects of the prepared Fe2O3 and CS/ε-Fe2O3 nanocomposites, including phase identification, determination of crystallite size, assessment of surface morphology, etc. CS/ε-Fe2O3 was drop-casted and deposited on the Screen-Printed Electrode (SPE). The resulting sensor exhibited excellent performance in the precise and selective quantification of Hg2+, Cd2+, and Pb2+ ions, with minimal interference from other substances. The fabricated sensor exhibits excellent performance as the detection range for Hg2+, Cd2+, and Pb2+ ions linearity is 2–20 μM, sensitivity, and LOD are 243 Ω/ μM cm2 and 0.191 μM, 191 Ω/μM cm2, and 0.167 μM, 879 Ω/ μM cm2, and 0.177 μM respectively. The stability of the CS/ε-Fe2O3/SPE electrode is demonstrated by checking its conductivity for up to 60 days for Hg2+, Cd2+, and Pb2+ ions. The reusability of the fabricated electrode is 14 scans, 13 scans, and 12 scans for Hg2+, Cd2+, and Pb2+ ions respectively. The findings indicate the successful development of an innovative CS/ε-Fe2O3 electrode for the EIS sensing platform. This platform demonstrates notable potential for addressing the critical need for efficient and sensitive EIS sensors capable of detecting a range of hazardous heavy metal ions, including Hg2+, Cd2+, and Pb2+.