A series of polymer nanocomposites (PNCs) based on the renewable poly(butylene-succinate) (PBSu) reinforced with 1 wt% of different nanoparticles (NP), namely, silica (SiO2), montmorillonite (MMT), graphene oxide (GO) and carbon nanotubes (CNT), were synthesized and studied herein. The investigation focuses on both the direct and indirect NP effects on the interfacial interactions, thermal transitions, crystallinity, electrical and thermal conductivity, mechanical properties and molecular dynamics. For that, a sum of complementary techniques was employed, regarding both the structure and performance. The clearly direct effect is related to the promotion of crystal nucleation at the presence of both particles, related to the fillers’ dimensionality (aspect ratio) and the non-worth noting interfacial interactions. The degree of crystallinity of PBSu mildly increases, whereas the semicrystalline morphology (sizes, numbers, distributions of the crystals) is systematically denser in the PNCs. In agreement with previous findings on PBSu, the polymer cannot be preserved amorphous, at least by conventional methods. Consequently, the macroscopic properties, namely, the thermal diffusivity/conductivity as well as the mechanical performance were found connected to crystallinity, in particular, to the semicrystalline morphology (indirect filler effect). PBSu/CNT was surprisingly found electrically conductive, despite the low CNT loading, whereas the rest of the samples are insulating. The molecular dynamics map was constructed here for the first time, obviously only for the semicrystalline state. The cooperativity of PBSu chains drops in the PNCs, most probably, affected by the dense semicrystalline structures that seem to impose an increase in the free volume of the amorphous polymer fraction. Overall, the PBSu PNCs were found to offer potentials for wide range manipulation of properties, via relatively mild processing (synthesis, thermal treatments).