Core-shell Au-Ag nanostructures (Au-AgNSs) are prepared by a seed-meditated growth, i.e., by a two-step process. The synthetic parameters greatly influence the morphologies of the final bimetallic Au-AgNSs, their stability and application potential as surface-enhanced Raman scattering (SERS) substrates. Direct comparison of several types of Au NPs possessing different surface species and serving as seeds in Au-AgNSs synthesis is the main objective of this paper. Borohydride-reduced (with varying stages of borohydride hydrolysis) and citrate-reduced Au NPs were prepared and used as seeds in Au-AgNSs generation. The order of reactants in seed-mediated growth procedure represents another key factor influencing the final Au-AgNSs characteristics. Electronic absorption spectra, dynamic light scattering, zeta potential measurements, energy dispersive spectroscopy and transmission electron microscopy were employed for Au-AgNSs characterization. Subsequently, possibilities and limitations of SERS-detection of unperturbed cationic porphyrin, 5,10,15,20-tetrakis(1-methyl-4-pyridyl)21H,23H-porphine (TMPyP), were investigated by using these Au-AgNSs. Only the free base (unperturbed) SERS spectral form of TMPyP is detected in all types of Au-AgNSs. It reports about a well-developed envelope of organic molecules around each Au-AgNSs which prevents metalation from occuring. TMPyP, attached via ionic interaction, was successfully detected in 10 nM concentration due to Au-AgNSs.