The deposition of multiphase materials with microstructural control would enable new fabrication modalities, such as spatial variation in composition and the integration of microstructure and structural features. In this work, acoustically-excited microfluidic print nozzles were used to tailor the microstructure of printed composite filaments consisting of SiC fibers, solid BaTiO3 spheres, or hollow SiO2 spheres in an epoxy matrix. The results demonstrate that acoustic focusing is a promising technique to control microparticles and deposit two-phase ordered structures using a single nozzle. In addition to tuning the microstructure within a single print line, the overall concentration of particles can be increased by focusing the particle stream in a branched geometry, enabling the deposition of material with higher particle volume fractions than the initial ink composition. We show that even modest volume fractions of acoustically-focused and concentrated SiC fibers can produce printed composite filaments with unprecedented control over microstructural ordering that exhibit strengths rivaling polymer-matrix composites with higher volume fractions of stiffer fibers.