A novel analytical strategy that couples enzyme-linked immunosorbent assay (ELISA) and electrochemical microfluidic chips to determine the mycotoxin zearalenone (ZEA) in baby foods is presented. The analytical cycles for an ultra-fast analysis of the sample and its sequential fast and simplified calibration were performed in about 200 s plus to ELISA protocol. This route avoided the typical four-parameter logistic curve fit which is a highly time-consuming and laborious procedure. An extremely low concentration level of ZEA (less than 1 ppb) was detected with reliability. This level is 20 times lower than the strictest tolerable limit (20 ppb) for baby foods, making the microfluidic approach the newly anticipated analytical security tool for the future. The reliability of the proposal was demonstrated by accuracy evaluations using a certified reference material and by demonstrating its suitability during the control of the regulatory limits of ZEA in baby foods. In addition, the microfluidic approach allowed sensitivity and the incubation enzymatic reaction to be manipulated in situ.