We aim to perform high-throughput (HT) dynamic structural studies on biomedically relevant proteins enabled by our technology development for time-resolved serial microcrystallography (TR-SMX) at the ESRF ID-29 microfocus beamline. Implementation of novel polymer-based sample supports (“chips”) will provide efficient sample introduction for TR-SMX measurements, serving two scientific thrusts: (1) determination of dynamic structure-function relationships in bacterial virulence factors important for intercellular pathogen infection and survival; (2) elucidation of energy-transfer structural mechanisms in a novel fluorescent protein used in sensing intercellular phenomena. Our microfluidic chips for TR-SMX will enable rapid sequential data collection from hydrated microcrystals at room temperature under optimized, protein-specific conditions. Our HT approach is expected to produce protein “molecular movies”, facilitating mechanism-based therapeutics and vaccine development.