During its infection cycle, Mycobacterium tuberculosis (Mtb) encounters changing environments within its eukaryotic host as it transitions between intra- and extracellular growth. Mtb is well adapted to navigate innate and adaptive immunity in different host niches to evade destruction and maintain growth. At all stages of infection, Mtb uses its unique cell surface to interact with the host, where the envelope acts as a multilayered barrier against host defences, modulates immune recognition and mediates cell-cell and host-pathogen interactions. Despite the importance of the cell envelope, we currently lack a detailed understanding of the structural principles that underpin its crucial role in Mtb survival during infection. To study how the mycobacterial cell surface performs its various roles in pathogenesis in a biologically relevant context, we have established new, correlative workflows that combine light microscopy and electron cryotomography (cryo-ET) to visualize M. marinum infections in zebrafish, its natural host and a well-established model for mycobacterial pathogenesis. Our workflows enable molecular-scale visualization of bacterial envelopes and their cellular interactions in a vitrified, near-native state. By integrating cryo-ET with volumetric cryo-scanning electron microscopy, live-cell confocal imaging and genetic screens, we describe key molecular principles of community organization that are critical for bacterial survival during infection. Together, this study establishes a powerful framework for in-tissue cryo-ET and correlative imaging to uncover the principles of bacterial infection across scales.