As the antimicrobial resistance crisis becomes a reality, we are only now realizing we lack a fundamental understanding of the mechanisms by which major pathogens infect their human host. To address this, we must employ novel methodologies that allow us to investigate microbial behavior in human infection-like contexts. Here, we present a framework for studying host-microbe interactions by integrating human-derived organoids with high-resolution live imaging and high-throughput sequencing technologies. This interdisciplinary and multiscale strategy has the potential to resolve host-microbe interactions in great detail under conditions replicating those encountered in vivo. Thus, infection studies based on organoid models could open new avenues for fundamental and translational research with therapeutic potential.