Microfluidic technologies are increasingly implemented to replace manual methods in biological and biochemical sample processing. We explore the feasibility of an acoustofluidic trap for confinement of microparticle reaction substrates against continuously flowing reagents in chemical synthesis and detection applications. Computational models are used to predict the flow and ultrasonic standing wave fields within two longitudinal standing bulk acoustic wave (LSBAW) microchannels operated in the 0.5-2.0 MHz range. Glass (gLSBAW) and silicon (siLSBAW) pillar arrays comprise trapping structures that augment the local acoustic field, while openings between pillars evenly distribute the flow for uniform exposure of substrates to reagents. Frequency spectra (acoustic energy density Eac vs frequency) and model-predicted pressure fields are used to identify longitudinal resonances with pressure minima in bands oriented perpendicular to the inflow direction. Polymeric and glass particles (10-and 20-μm diameter polystyrene beads, 6 μm hollow glass spheres, and 5 μm porous silica microparticles) are confined within acoustic traps operated at longitudinal first and second half-wavelength resonant frequencies (f1,E = 575 kHz, gLSBAW; f1,E = 666 kHz; and f2,E = 1.278 MHz, siLSBAW) as reagents are introduced at 5-10 μl min-1. Anisotropic silicon etched traps are found to improve augmentation of the acoustic pressure field without reducing the volumetric throughput. Finally, in-channel synthesis of a double-labeled antibody conjugate on ultrasound-confined porous silica microparticles demonstrates the feasibility of the LSBAW platform for synthesis and detection. The results provide a computational and experimental framework for continued advancement of the LSBAW platform for other synthetic processes and molecular detection applications.