In situ synchrotron X-ray scattering was used to reveal the transient microstructure of poly(L-lactide) (PLLA)/tungsten disulfide inorganic nanotubes (WS2NTs) nanocomposites. This microstructure is formed during the blow molding process (“tube expansion”) of an extruded polymer tube, an important step in the manufacturing of PLLA-based bioresorbable vascular scaffolds (BVS). A fundamental understanding of how such a microstructure develops during processing is relevant to two unmet needs in PLLA-based BVS: increasing strength to enable thinner devices and improving radiopacity to enable imaging during implantation. Here, we focus on how the flow generated during tube expansion affects the orientation of the WS2NTs and the formation of polymer crystals by comparing neat PLLA and nanocomposite tubes under different expansion conditions. Surprisingly, the WS2NTs remain oriented along the extrusion direction despite significant strain in the transverse direction while the PLLA crystals (c-axis) form along the circumferential direction of the tube. Although WS2NTs promote the nucleation of PLLA crystals in nanocomposite tubes, crystallization proceeds with largely the same orientation as in neat PLLA tubes. We suggest that the reason for the unusual independence of the orientations of the nanotubes and polymer crystals stems from the favorable interaction between PLLA and WS2NTs. This favorable interaction leads WS2NTs to disperse well in PLLA and strongly orient along the axis of the PLLA tube during extrusion. As a consequence, the nanotubes are aligned orthogonally to the circumferential stretching direction, which appears to decouple the orientations of PLLA crystals and WS2NTs.