This work reports on the design and development of nanocomposites based on a polymeric matrix containing biodegradable Polylactic Acid (PLA) and Polyhydroxyalkanoate (PHA) coated with either Graphite NanoPlatelets (GNP) or silver nanoparticles (AgNP). Nanocomposites were obtained by mechanical mixing under mild conditions and low load contents (<0.10 wt %). This favours physical adhesion of the additives onto the polymer surface, while the polymeric bulk matrix remains unaffected. Nanocomposite characterisation was performed via optical and focused ion beam microscopy, proving these nanocomposites are selectively modified only on the surface, leaving bulk polymer unaffected. Processability of these materials was proven by the fabrication of samples via injection moulding and mechanical characterisation. Nanocomposites showed enhanced Young modulus and yield strength, as well as better thermal properties when compared with the unmodified polymer. In the case of AgNP coated nanocomposites, the surface was found to be optically active, as observed in the increase of the resolution of Raman spectra, acquired at least 10 times, proving these nanocomposites are promising candidates as surface enhanced Raman spectroscopy (SERS) substrates.