This work addresses a novel, rapid and cost-effective approach for the electrochemical sensing of scombrotoxin (histamine) in fish based on magnetic molecularly imprinted polymer (magnetic-MIP). The histamine magnetic-MIP was synthesized by the core-shell method using histamine as a template, and 2-vinyl pyridine as functional monomer. The magnetic-MIP was characterized by TEM, SEM, and confocal microscopy. Additionally, the binding capacity of magnetic-MIP towards histamine was investigated and compared with magnetic non-molecularly imprinted polymer (magnetic-NIP). This biomimetic material merged the advantages of MIPs and magnetic particles (MPs), including low cost of production, stability, high binding capacity and can be easily separated by the aid of a permanent magnet. The magnetic-MIP was integrated into magneto-actuated electrodes for the direct electrochemical detection of histamine preconcentrated from fish samples. The results revealed that this approach succeeded in the preconcentration and determination of histamine with a LOD as low as 1.6 × 10−6 mg L−1, much lower than the index for fish spoilage (50 mg kg−1) accordingly to the legislation. Furthermore, the analytical performance was validated for the determination of histamine in scombroid fish samples with recovery values ranging from 96.8 to 102.0 %, confirm so it can be applied easily for routine food examination.