The development of a highly sensitive electrochemical sensor (E-sensor) is described based on stand-alone plastic electrodes (PE) for phosphate detection, being an essential nutrient in the marine environment. The detection mechanism is based on the chemical affinity between polyoxomolybdate anions (POM) and orthophosphate to form an electroactive phosphomolybdate complex. The custom-made E-sensor was formulated with an organic octamolybdate derivative (TBA4Mo8O26) incorporated with periodic mesoporous organosilica (PMO) to obtain a significant improvement in the analytical performances of phosphate determination. This POM@PMO combination was found to be advantageous in the determination of low concentrations of phosphate in standard solutions ranging from 1 to 500 nM, using square wave voltammetry as the detection technique. This sensitivity enhancement can be attributed to the effect of hydrophobic PMO in loading more POM moieties, owing to its highly porous structure and charged shell. Consequently, the POM@PMO-PE sensor achieved a competitive sensitivity of 4.43 ± 0.14 μA.nM−1.cm−2 and a limit of detection of 0.16 nM with good selectivity against silicates. Finally, seawater and treated wastewater samples have been tested to validate the sensor response in comparison to the official method of phosphate determination.Graphical abstract