A highly sensitive method for the determination of aflatoxin M1 (AFM1) is described that involves the use of a disposable multichannel microplate coupled to intermittent pulse amperometry (IPA) for immunosensor development based on a direct competitive assay. Immunoassay parameters were evaluated and optimized to establish an electrochemical enzyme-linked immunosorbent assay (ELISA) procedure for AFM1 in milk samples. The suitability of the immunosensors for the direct analysis of the toxin in milk was assessed. AFM1 was measured with a working range of 5–250 pg mL−1 and a detection limit of 1 pg mL−1. Good recovery values (90–105%) were obtained. The method was used to study the recovery of this toxin in frozen (−30 °C) or lyophilized (4 °C) milk samples stored for up to 3 months. A significant, but variable, decrease (>50%) of the measured AFM1 concentration with respect to the initial toxin contamination levels was found.