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In this work, MIL-100(Fe)-decorated mesoporous carbon powders (MC@MIL-100(Fe)) were prepared by in situ growth of MIL-100(Fe) on the surface of ZIF-8 framework-based mesoporous carbons (MC). The hybrid material was characterized using SEM equipped with EDS mapping for morphology investigation, X-ray photoelectron spectroscopy for chemical valence analysis, and X-ray diffraction for crystal structure determination. The developed sensor separated from the traditional bismuth film decoration, and simultaneously, MC@MIL-100(Fe) was applied for the first time to electrochemically detect trace amounts of Pb(II) and Cd(II). The fabricated MC@MIL-100(Fe)-based electrochemical sensor showed excellent response to the target analytes at –0.55 and − 0.75 V for lead and cadmium ions, respectively. By adjusting some measurement parameters, that is, the loading concentration of MC@MIL-100(Fe), acidity of the HAc-NaAc buffer (ABS), deposition potential, and deposition time, the analytical performance of the proposed electrochemical sensor was examined by exploring the calibration curve, repeatability, reproducibility, stability, and anti-interference under optimized conditions. The response current of the proposed MC@MIL-100(Fe) electrochemical sensor showed a well-defined linear relationship in the concentration ranges of 2–250 and 2–270 μg·L−1 for Cd(II) and Pb(II), respectively. In addition, the detection limits of the sensor for Cd(II) and Pb(II) were 0.18 and 0.15 μg L−1, respectively, which are well below the World Health Organization (WHO) drinking water guideline value. The MC@MIL-100(Fe) can be potentially used as an electrochemical platform for monitoring heavy metals in surface water, with satisfactory results.