In the present study, the immobilization of sulfonic acid on polythiophene (PTh)‐layered magnetite was carried out through the reaction of ClSO3H with Fe3O4‐PTh. The obtained catalyst, Fe3O4‐PTh‐SO3H, as the reusable and novel magnetic heterogeneous nanocatalyst, was used for green synthesis of 2,4,5‐trisubstituted‐1H‐imidazoles, and 2‐(1H‐tetrazole‐5‐yl) acrylonitriles. The catalyst structure was characterized by various techniques, including FT‐IR, XRD, SEM, EDX, TEM, VSM, ICP‐OES, and CHNS techniques. These analyses proved the sulfonic group's successful attachment on the outer surface of the nanocatalyst. A high number of the acidic groups on the surface of the PTh layer are conducted to the more active catalyst, and as a result, the yield of the target product increases. The sustainability of the methodology was examined by evaluating the stability and reusability of the catalyst using an external magnet. The results showed that the Fe3O4‐PTh‐SO3H catalyst could be reused for five successive runs without a significant loss in catalytic efficiency. The reactions were carried out under relatively mild conditions in ethanol to achieve imidazole and tetrazole derivatives in high to excellent yields.