The promising fluorescent nature and functional properties of gold nanoclusters (AuNCs) enable their use as efficient sensor probes in various fields, particularly in healthcare diagnostics. Together with the effective fluorescence property, AuNCs also possess efficient electrocatalytic activity toward biosensing, thereby featuring the dual-functional (fluorescent and electrochemical) immunoprobe for sensing SARS-CoV-2 nucleoprotein. Density functional theory (DFT) calculations were carried out to assess the electronic structure arrangement of gold (III) chloride and bovine serum albumin (BSA) interactions with gold for efficient formation of Au clusters. Structural studies of coupled AuNCs show that antibodies with active sites for antigen binding are well conjugated on the surface of the gold nanoclusters. X-ray photoelectron and ultraviolet photoelectron spectral studies exhibited that the progression of the work function and ionization energy of nucleocapsid antibody conjugated AuNCs support antigen detection. The bio-affinitive nature of the AuNCs advances the mending of antibodies on their surface so as to increase the binding with epitopes of SARS-CoV-2 nucleoprotein. Antibody conjugated AuNCs based dual sensing system displayed an effective linear response with the lowest detection limit of about 20 pM and exhibited high responsiveness toward nucleoprotein detection. Thus, the dual practical sensing platform constructed from gold nanocluster-derived nanostructures offers new knowledge for additional examinations of COVID-19 detection.