While bioengineers ask how the shape of diagnostic and therapeutic particles impacts their pharmacological efficiency, biodistribution, and toxicity, microbiologists suggested that morphological adaptations enable pathogens to perhaps evade the immune response. Here, a shape-dependent process is described that limits phagocytosis of filamentous Escherichia coli bacteria by macrophages: successful uptake requires access to one of the terminal bacterial filament poles. By exploiting micropatterned surfaces, we further demonstrate that microenvironmental heterogeneities can slow or inhibit phagocytosis. A comparison to existing literature reveals a common shape-controlled uptake mechanism for both high-aspect ratio filamentous bacteria and engineered particles.