In this study, a heterogeneous nanocatalyst is presented that is capable to efficiently catalyze the synthetic reactions of amide bond formation between the amino acids. This nanocatalyst which is named Fe3O4@SiO2/TABHA (TABHA stands for thio-aza-bicyclo-hepten amine), was composed of several layers that increased the surface area to be functionalized with 2-aminothiazole rings via Diels–Alder approach. Firstly, various analytic methods such as Fourier-transform infrared (FTIR) and energy-dispersive X-ray (EDX) spectroscopic methods, thermogravimetric analysis (TGA), electron microscopy (EM), and UV–vis diffuse reflectance spectroscopy (UV-DRS) have been used to characterize the desired structure of the Fe3O4@SiO2/TABHA catalyst. Afterward, the application of the presented catalytic system has been studied in the peptide bond formation reactions. Due to the existence of a magnetic core in the structure of the nanocatalyst, the nanoparticles (NPs) could be easily separated from the reaction medium by an external magnet. This special feature has been corroborated by the obtained results from vibrating-sample magnetometer (VSM) analysis that showed 24 emu g−1 magnetic saturation for the catalytic system. Amazingly, a small amount of Fe3O4@SiO2/TABHA particles (0.2 g) has resulted in ca. 90% efficiency in catalyzing the peptide bond formation at ambient temperature, over 4 h. Also, this nanocatalyst has demonstrated an acceptable recycling ability, where ca. 76% catalytic performance has been observed after four recycles. Due to high convenience in the preparation, application, and recyclization processes, and also because of lower cost than the traditional coupling reagents (like TBTU), the presented catalytic system is recommended for the industrial utilization.