In this study, we demonstrate the use of micro-/nano-layer (MNL) extrusion technology to tune the mechanical properties of polypropylene (PP)/polyethylene terephthalate (PET) fibrillar blends. Nano-fibril-in-microfiber composites, with 3, 7, and 15 wt.% PET, are prepared using a spunbond system, and then fed into an MNL extrusion system to be subjected to strong shear and extensional flow fields in the multipliers. Preferential alignment of the PET nano-fibrils is confirmed via morphological observations using scanning electron microscopy. Additionally, increasing the mass flow rate is shown to further increase the degree of fibril orientation along the machine direction (MD). Tensile tests revealed that for each PET loading, the elastic modulus and yield strength of the composites are significantly enhanced with increasing number of multipliers and mass flow rate, while such mechanical enhancement is accompanied by a slight sacrifice in ductility. Overall, MNL extrusion is a promising technology to further enhance mechanical properties of nano-fibril composites.