Correlated electronic systems are naturally susceptible to develop collective, symmetry-breaking electronic phases as observed in Cu- and Fe-based high-temperature superconductors, and twisted Moiré superlattices. The family of kagome metals AV3Sb5 (A = K, Rb, Cs) is a recently discovered, rich platform to study many of these phenomena and their interplay. In these systems, three-dimensional charge order (3D-CO) is the primary instability that sets the stage in which other ordered phases emerge, including unidirectional stripe order, orbital flux order, and superconductivity. Therefore, determining the exact nature of the 3D-CO is key to capture the broader phenomenology in AV3Sb5. Here, we use high-resolution angle-resolved photoemission spectroscopy to resolve the microscopic structure and symmetry of 3D-CO in AV3Sb5. Our approach is based on identifying an unusual splitting of kagome bands induced by 3D-CO, which provides a sensitive way to refine the spatial charge patterns in neighboring kagome planes. Notably, we found a marked dependence of the 3D-CO structure on alkali metal and doping: the 3D-CO in CsV3Sb5 is composed of kagome layers with alternating Star-of-David and Tri-Hexagonal distortions, while KV3Sb5, RbV3Sb5, and Sn-doped CsV3Sb5 realize a staggered charge pattern breaking C6 rotational symmetry. These results establish the microscopic structure of 3D-CO and its evolution with chemical composition for the first time, providing fresh insights on the origin of the cascade of exotic electronic phases in AV3Sb5.