The super paramagnetic iron oxide nanoparticles (SPIONs) such as magnetite (Fe3O4) appear as an emerging class of materials in the field of environmental remediation owing to its biocompatibility, high surface area, super paramagnetic properties and ease of reuse and recovery. However, susceptibility of bare Fe3O4 to oxidation and agglomeration limits its use as an adsorbent material in aqueous medium, which demands the surface capping of these Fe3O4 nanoparticles for effective adsorption performance. We have successfully capped Fe3O4 with sodium citrate with a purpose to develop a felicitous magnetic sorbent material containing abundant metal trap centers at its surface. The successful surface modification of Fe3O4 with citrate is noticeable from FT-IR, TGA, XRD, Zeta potential (DLS), SEM, EDX,TEM, DR-UV, and contact angle measurements. For the first time, we report electrical impedance spectroscopic studies on this capped magnetic nanoparticle to understand the capacitive behavior of super paramagnetic Fe3O4 and citrate@Fe3O4 nanoparticles. The cyclic voltammograms manifested the excellent electrochemical response of citrate@Fe3O4 modified glassy carbon electrode to mM concentrations of Pb2+, Cd2+ and Zn2+ ions with response in order Pb2+> Cd2+> Zn2+. Differential Pulse Voltammetry confirms the descent sensitivity towards Pb2+ ions at different concentration with a 0.3 µM detection limit. The adsorption of Pb2+ ions followed Langmuir isotherm model with maximum monolayer adsorption capacity of 58.93 mg g−1. To further validate the experimental adsorption results and the mode of interaction between Pb2+and citrate@Fe3O4, quantum calculations using density functional theory were performed which indicate a good coherence between experimental and theoretical data. The presence of abundant carboxyl and hydroxyl metal trap centers at the surface of citrate@Fe3O4 is responsible for its promising adsorption capacity for Pb2+ ions removal. Both experimental as well as theoretical results suggest that surface functionalization has a positive impact for detection of heavy metal ions and should be given prime importance while designing absorbent materials. The citrate@Fe3O4 nanoparticles exhibit outstanding stability and regeneration over various cycles of sorption.