Nivalenol as a mycotoxin pesticide is toxic to humans and animals and causes major health problems including hemorrhage, anemia, and vomiting. Thus, the need for fast and reliable analytical systems in terms of the management of health risks resulting from nivalenol exposure has increased in recent years. The aim of this study involved a novel molecularly imprinted quartz crystal microbalance sensor preparation based on sulphur-incorporating cobalt ferrite for nivalenol detection in rice samples. For this aim, cobalt ferrite and sulfur incorporated cobalt ferrite were successfully synthesized by sol–gel and calcination methods, respectively. Then, nivalenol imprinted quartz crystal microbalance chips based on cobalt ferrite and sulfur incorporated cobalt ferrite were prepared by an ultraviolet polymerization technique including N,N′-azobisisobutyronitrile as the initiator, ethylene glycol dimethacrylate as the cross-linker, methacryloylamidoglutamic acid as the monomer, and nivalenol as the analyte. After some spectroscopic, electrochemical and microscopic characterization studies, the developed sensor was applied to rice grain samples for the determination of nivalenol. The linearity of the prepared sensor was observed to be 1.0–10.0 ng L⁻¹ and the limit of quantification and detection limit were found to be 1.0 and 0.33 ng L⁻¹, respectively. Finally, the high selectivity, repeatability, and stability of the prepared sensor based on sulphur-incorporating cobalt ferrite and a molecularly imprinted polymer can ensure safe food consumption worldwide.