Ternary blends of polylactide (PLA, 90 wt.%) and poly(methyl methacrylate) (PMMA, 10 wt.%) with functionalized polysilsesquioxanes (LPSQ-R) were obtained by solution blending. R groups in LPSQ containing hydroxyethyl (LPSQ-OH), methylglycolic (LPSQ-COOMe) and pentafluorophenyl (LPSQ-F5) moieties of different chemical properties were designed to modify PLA blends with PMMA. The effect of the type of LPSQ-R and their content, 1–3 wt.%, on the structure of the blends was studied with scanning electron microscopy (SEM) combined with energy dispersive spectroscopy (SEM-EDS), dynamic mechanical thermal analysis (DMTA) and Raman spectroscopy. Differential scanning calorimetry (DSC) and tensile tests also showed various effects of LPSQ-R on the thermal and mechanical properties of the blends. Depth-sensing indentation was used to resolve spatially the micro- and nano-scale mechanical properties (hardness and elastic behaviour) of the blends. The results showed clearly that LPSQ-R modulate the structure and properties of the blends.