In this research, an efficient and simple method has been reported for the preparation of spiro[indene[1,2‐d]pyrimidine‐one derivatives through the multi‐component reactions of cyclic ketones, urea/thiourea/guanidine and 1,3‐indandion in the presence of NiCo2O4@Ni(BDC) (terephthalic acid) nanocatalyst. In this method, the products were obtained in short reaction times and excellent yields. The prepared metal‐organic frameworks have been fully analyzed by fourier transform infrared spectrophotometry (FT‐IR), field emission scanning electron microscopy (FE‐SEM), energy‐dispersive X‐ray spectroscopy (EDX), thermogravimetric analysis (TGA),vibrating sample magnetometry (VSM), transmission electron microscopy (TEM), N2 adsorption‐desorption by Brunauer–Emmett‐Teller (BET) and X‐ray diffraction (XRD)analysis. In addition, all of the synthesized pyrimidines screened against different pathogenic bacteria including Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa and also their antifungal activity were investigated against Candida albicans.