Developing new ultrasensitive assays for the detection of the presence, and determination of the serotype of the most poisonous material known i.e. botulinum neurotoxin (BoNT) is vital to human health and the wellbeing of the surrounding environment. Here, an electrochemical sandwich immunoassay with high sensitivity is adopted to achieve simultaneous determination of BoNT serotypes A and E based on polystyrene@polydopamine/Cd2+ and Ag nanoparticles acting as monoclonal antibody labels. Two well-separated peaks with strong electrochemical signals are generated by the labels, allowing for the simultaneous detection of two analytes existing on the electrode. To obtain well-oriented polyclonal antibodies immobilization, boronic acid is directly attached to the magnetic core/metal-organic framework (MOF) shell nanoagent surfaces without the requirement of a long and flexible spacer. Accordingly, it is possible to directly detect the metal ion labels through square wave voltammetry without the metal pre-concentration step. This results in distinct and well-defined voltammetric peaks, pertaining to each sandwich-type immunocomplexes. The limits of detection of BoNT/A and BoNT/E analyses were found to be 0.04 and 0.16 pg mL− 1 with the linear dynamic ranges of 0.1–1000 and 0.5–1000 pg mL− 1 , respectively. Based on the obtained results, this immunosensor has the wide linear ranges, while also exhibiting low limits of detection along with good stability and reproducibility.