A label-free electrochemical immunosensor using a toluidine blue (TB)/porous organic polymer (POP)/two-dimensional molybdenum diselenide (2D MoSe2) nanocomposite is developed for highly sensitive detection of aflatoxin B1 (AFB1) in selected crops. A POP/2D MoSe2 composite material is employed to modify the surface of a screen-printed carbon electrode (SPCE). Subsequently, TB is adsorbed on the modified SPCE surface, and the resulting TB/POP/2D MoSe2 composite is then used to construct a biosensor. The new POP/2D MoSe2 nanocomposite offers a high surface-to-volume area and is a good electroactive and biocompatible adsorbent for loading TB probe and capture antibodies. Adsorbed TB onto the POP/2D MoSe2 nanocomposite is utilized as a redox probe for the signal amplification unit. This TB/POP/2D MoSe2 nanocomposite provides good electron transfer properties of TB redox probe, good electrical conductivity, good biocompatibility, and likable adsorption ability, thus obtaining a sufficient immobilization quantity of antibodies for the sensor construction. After immobilization of the anti-AFB1 antibody and blocking with BSA on the composite surface, the immunosensor is obtained for the detection of AFB1. Under optimum conditions, the sensor shows a linear logarithmic range of 2.5–40 ng mL−1 with a limit of detection (LOD) of 0.40 ng mL−1. The developed sensor provides several advantages in terms of simplicity, low cost, short analysis time, high selectivity, stability, and reproducibility. Additionally, the proposed immunosensor is successfully validated by the detection of AFB1 in rice, corn, and peanut samples. Utilizing the TB/POP/2D MoSe2 nanocomposite, this label-free electrochemical immunosensor demonstrates outstanding sensitivity and selectivity in detecting AFB1, making it a valuable tool for ensuring the safety of agricultural products and enhancing food security.