The synthesis of two series of poly(lactic acid) (PLA)-based polymer nanocomposites (PNCs) filled with small amounts (0.5 and 1%) of Ag and Cu nanoparticles (NPs) was performed. Moreover, two methods for the PNC synthesis were performed, namely, ‘conventional mixing techniques’ and ‘in situ ring opening polymerization (ROP)’. The latter method was employed for the first time; moreover, it was found to be more effective in achieving very good NP dispersion in the polymer matrix as well as the formation of interfacial polymer–NP interactions. The in situ ROP for PLA/Cu was not productive due to the oxidation of Cu NPs being faster than the initiation of ROP. The presence of NPs resulted in suppression of the glass transition temperature, Tg (23–60 °C), with the effects being by far stronger in the case of ROP-based PNCs, e.g., exhibiting Tg decrease by tens of K. Due to that surprising result, the ROP-based PLA/Ag PNCs exhibited elevated ionic conductivity phenomena (at room temperature). This can be exploited in specific applications, e.g., mimicking the facilitated small molecules permeation. The effects of NPs on crystallinity (2–39%) were found opposite between the two series. Crystallinity was facilitated/suppressed in the mixing/ROP -based PNCs, respectively. The local and segmental molecular mobility map was constructed for these systems for the first time. Combining the overall data, a concluding scenario was employed, that involved the densification of the polymer close to the NPs’ surface and the free volume increase away from them. Finally, an exceptional effect was observed in PLA + 0.5% Ag (ROP). The crystallization involvement resulted in a severe suppression of Tg (−25 °C).