This paper presents a new method for detecting malathion pesticides using a modified screen-printed electrode (SPE) with a fluorescence quenching technique. The manganese-based MOF was synthesized using the solvothermal method. The synthesized MOFs were characterized by transmission electron microscopy (TEM), x-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), and Raman spectroscopy. The material’s electrocatalytic properties were assessed via electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV). Within the concentration range of 0.89 µM to 5.95 µM, the material’s response to malathion was analyzed with square wave voltammetry (SWV), giving rise to a detection limit of 39.097 nM. Fluorescence quenching studies have been carried out between 0.039 and 0.56 µM, with a lower detection limit of 62.03 nM. A sensor with good anti-interference properties was tested for selectivity and practicability in detecting malathion in real samples, proving its potential use in this area.