A novel sandwich-structured composite was developed from the surface layers of polyhydroxyalkanoate (PHA) and the interlayer of polylactic acid (PLA)/cellulose microfibers (CMF) composite. Moreover, CMF was chemically modified via a sol–gel process to improve the compatibility between the natural reinforcement and the polymer matrix. According to the obtained results, the modified CMF exhibited a highly hydrophobic characteristic (contact angel value of approximately 118°), and they were homogeneously dispersed in the PLA matrix. The results of the thermogravimetric analysis indicated that the sandwich composites reinforced with the modified CMF showed improvement in thermal stability. Regarding the mechanical properties, the incorporation of the natural reinforcement into sandwich composites increased the values of tensile modulus and strength of materials. The water vapor permeability of sandwich composites increased with the addition of untreated fibers; however, the composites reinforced with the modified CMF showed superior barrier performance than that of untreated CMF. In addition, a durability test was performed to determine the effect of accelerated aging on the properties of sandwich composites. The results demonstrated that the mechanical and barrier properties of composites incorporated with untreated CMF decreased after the accelerated aging, whereas the composites reinforced with the modified CMF experienced the least change.