Polybrominated diphenyl ethers (PBDEs) are persistent environmental substances that were commonly used as fire retardants in a wide number of commercial products. Their low reactivity, high hydrophobicity and bioaccumulative properties cause their ubiquity in the air, water, food and lead to extensive exposure of world population to these compounds. The severe health problems caused by PBDEs lead them to be banned from the market. In March 2014 the European Commission issued a recommendation in which member states are requested to monitor brominated flame retardants in food, in order to evaluate human and wildlife exposure. Here, we described the development of an electrochemical magnetic particle enzyme‐linked immunoassay to analyze PBDEs in food samples. The immunological reaction is based on a competitive scheme, using an alkaline phosphatase labeled congener as tracer. The anti‐PBDE antibody modified magnetic particles are captured on the surface of carbon disposable array of sensors. The reaction extent is finally electrochemically measured by differential pulse voltammetry, upon the addition of substrate. Under the optimized conditions, a limit of detection of 0.18 ng/mL with a limit of quantification of 0.30 ng/mL and a quantification range of 0.30–6.9 ng/mL, (RSD%=12) is obtained. Results of food samples obtained from the newly developed electrochemical immunoassay are also reported.