Surface-enhanced Raman scattering (SERS) nano-tags are of increasing interest in biomedical research as viable alternatives to bio-imaging techniques based on semiconductor quantum dots or fluorescent molecules. In this work, we fabricate silica-coated gold nanorods (AuNRs) encoded with two molecular labels to operate as highly effective spectroscopic nano-tags in near-infrared SERS (NIR-SERS) and surface-enhanced resonance Raman scattering combined with metal-enhanced fluorescence (SERRS-MEF), respectively. Specifically, a non-fluorescent molecule with strong affinity for a gold surface (para-aminothiophenol, p-ATP) and a common dye (Nile Blue, NB) with lower affinity have been successfully tested as NIR-SERS nano-tags under laser excitation at 785 nm. Moreover, as a result of designing AuNRs with a plasmon resonance band overlapping the electronic absorption band of the encoded NB molecule, a dual SERRS and MEF performance has been devised under resonant excitation at 633 nm. We explain this result by considering a partial desorption of NB molecules from the metal surface and their trapping into the silica shell at favorable distances to avoid quenching and enhance the fluorescence signal. Finally, we prove that the silica shell prevents the desorption or chemical transformation of p-ATP into p,p'-dimercaptoazobenzene species, as previously noticed, thus providing a highly stable SERRS signal, which is crucial for imaging applications.