Mycotoxins are causing persistent worries regarding food safety worldwide due to their ability to elicit a wide range of harmful effects in both animals and humans. Approaches that can identify a single mycotoxin are not sufficient for addressing the needs of quality control of agricultural products since they are often co-contaminated by multiple mycotoxins. This paper presents the development of an electrochemical sensor that is free of biomolecules and is capable of simultaneously detecting zearalenone (ZEN) and ochratoxin A (OTA) through the incorporation of nickel oxide (NiO) with carboxylated carbon nanotubes (MWCNT(–COOH)).This is the first time that NiO–MWCNT(–COOH) based electrochemical sensor has achieved the simultaneous potential-resolved selective detection of ZEN and OTA. Under optimized conditions, good linear responses were observed in the range of 0.01–10.24 μg mL−1 for ZEN and 0.04–10.24 μg mL−1 for OTA with low detection limit of 6 and 15 ng mL−1, respectively. The proposed electrochemical sensor demonstrated good selectivity, reusability, reproducibility, and shelf-life for the sensitive detection of both mycotoxins. Moreover, the sensor was made utilizing screen-printing technology to demonstrate its potential for commercialization and practical application. Our biomolecule-free electrochemical sensor was successful in evaluating these mycotoxins in actual samples of corn flour and wheat flour, proving its promising application in monitoring ZEN and OTA co-contamination in agricultural products.