Multimodal imaging agents derived from plasmonic nanoparticles have great potential for medical diagnostics. To date, dual-mode Raman-fluorescence gold-based nanolabels have remained outside conformed in vivo studies. To overcome this lack, gold nanorods coated by a polymer shell with incorporated cyanine 7 and a bimodal optical response were prepared. The study of nanolabels imaging capabilities was performed after their intravenous administration to laboratory mice. Natural biodistribution of the labels was obtained from SERS spectra of tissue sections, fluorescence images of organs, and gold concentrations determined in the digested tissues by ICP-AES. The comparison of distribution diagrams obtained from three techniques revealed that fluorescence tomography gives the underestimated labels content in the spleen, arising as a result of emission self-quenching. The consistency of SERS and ICP-AES results opens up the opportunity to use SERS as a complementary technique to assess semi-quantitative gold nanoparticle distribution in the tissues.