Composites based on anL-rich poly(lactic acid) (PLLA) and MCM-41, either neat or modified with a silver (MCM-41@Ag), are achieved by solvent casting, being next processed by compression molding. Ag is mainly embedded as nanowires within the hybrid MCM-41@Ag particles, enabling its antimicrobial character. In these composites, the PLLA thermal stability, nucleation efficiency, and mechanical response are dependent on the MCM-41 nature and, to a lesser extent, on its content. Thus, differences in transitions of the PLLA matrix are noticed during cooling at 10 °C/min and in the subsequent heating when composites with neat or modified MCM-41 are compared. A very remarkable nucleation effect is played by pristine MCM-41, being inferior when MCM-41@Ag is incorporated into the PLLA. Wide angle X-ray scattering (WAXS) measurements using synchrotron radiation and performed under variable-temperature conditions in the composites containing MCM-41@Ag indicate that during cold crystallization, the disordered α′ polymorph is initially formed, but it rapidly transforms into ordered α crystals. A long spacing peak, clearly seen in pure PLLA, appears as a small shoulder in PLLAMCM@Ag4 and is undetectable in PLLAMCM@Ag9 and PLLAMCM@Ag20. Furthermore, an increase in MH with the silica content is found in the two sets of composites, the higher MH values being observed in the family of PLLA and MCM-41@Ag. Finally, remarkable antimicrobial features are noticeable in the composites with MCM-41@Ag since this modified silica transfers its biocidal characteristics into the PLLA composites.