Fe3O4@MCM‐41@Zr‐MNPs modified with piperazine is easily prepared and characterized using Fourier transform infrared spectroscopy (FT‐IR), X‐ray powder diffraction (XRD), N2 adsorption–desorption, Transmission electron microscopy (TEM), Energy‐dispersive X‐ray (EDX), Vibrating sample magnetometry (VSM) and Thermogravimetric analysis (TGA) techniques. The characterization results showed that Zr highly dispersed in the tetrahedral environment of silica framework and piperazine is successfully attached to the surface of the nanocatalyst in connection with zirconium. The prepared nanosized reagent (10–30 nm), shows excellent catalytic activity in the synthesis of tetrahydro‐4H‐chromene and pyrano[2,3‐d]pyrimidinone derivatives. All reactions are performed under mild and completely heterogeneous reactions conditions in high yields during short reaction times. On the other hand and due to its superparamagnetic nature the catalyst can be easily separated by the application of an external magnetic field and reused for several times.