Bacterial motility is central to processes in agriculture, the environment, and medicine. While motility is typically studied in homogeneous environments, many bacterial habitats—e.g., soils, sediments, and biological gels/tissues—are heterogeneous porous media. Here, through studies of E. coli in transparent 3D porous media, we demonstrate that confinement in a heterogeneous medium fundamentally alters motility. In particular, we show how the paradigm of run-and-tumble motility is dramatically altered by pore-scale confinement, both for cells performing undirected motion and those performing chemotaxis, directed motion in response to a chemical stimulus. Our porous media also enable precisely structured multi-cellular communities to be 3D printed. Using this capability, we show how confinement-dependent chemotaxis enables populations to stabilize large-scale perturbations in their overall morphology. Together, our work thus reveals new principles to predict and control the behavior of bacteria, and active matter in general, in heterogeneous environments.