5-Hydroxymethyl furfural (HMF) is an intermediate produced by dehydrating sugars, such as fructose, sucrose, and glucose, in an acidic medium or during the Maillard reaction. It also occurs due to the storage of sugary foods at inappropriate temperatures. In addition, HMF is seen as a quality criterion in products. In this study, a novel molecularly imprinted electrochemical sensor based on graphene quantum dots incorporated NiAl2O4 (GQDs-NiAl2O4) nanocomposite was presented for the selective determination of HMF in coffee samples. Various microscopic, spectroscopic, and electrochemical methods were carried out for the structural characterizations of GQDs-NiAl2O4 nanocomposite. The molecularly imprinted sensor was prepared by multi-scanning using cyclic voltammetry (CV) in the presence of 100.0 mM pyrrole monomer and 25.0 mM HMF. After method optimization, the sensor revealed linearity towards HMF in the range of 1.0-10.0 ng L-1 with a detection limit (LOD) of 0.30 ng L-1. The developed MIP sensor's high repeatability, selectivity, stability, and fast response ability can provide reliable HMF detection in beverages, such as coffee, which is heavily consumed.