Colloidal crystals are encountered in a variety of energy-harvesting applications, where they serve as waveguides or filters for electromagnetic and electro-optic energy. Techniques such as electric or magnetic assembly are used to assemble colloidal crystals, but are limited by crystal size, yield, and throughput. This article demonstrates the continuous, high-throughput assembly of two-dimensional (2D)-colloidal crystals in an acoustofluidic flow cell. The device is fabricated using off-the-shelf components and does not require a clean-room access. An experimental state diagram shows how the fluid flow rate and voltage applied to the piezoelectric element in our device can tune the crystal microstructure. Highly ordered colloidal crystals are continuously assembled in less than a minute with a throughput yield of several hundred particles per minute using this device. The acoustically assembled ordered 2D crystals are immobilized using a UV-curable resin and extracted as ordered polymer-particle fibers, demonstrating the ability of using acoustic fields to assemble ordered structures embedded in bulk materials. Particle tracking is used to construct the cross-channel particle distribution to understand the effect of acoustic compression on colloidal crystal assembly. Microparticle image velocimetry data is compared to a theoretical transport model to quantify the effect fluid flow and acoustic trapping has on the colloidal crystal ensemble.