Hydrogel materials and scaffolds have emerged as transformative tools in biological research by offering control and customization of cell viability, metabolism, and productivity. Their compatibility with 3D bioprinting and patterning technologies enables the precise and reproducible organization of living components, ushering in novel experimental paradigms across diverse disciplines. Although most 3D hydrogel research has emphasized mammalian cell applications, particularly in tissue engineering, there is a growing body of research applying these technologies to study, manipulate, and harness a variety of microorganisms, such as bacteria. This review surveys the latest advances in microbial hydrogel encapsulation, focusing on material selection and patterning methods designed to preserve microbial viability and function. We compare the distinct requirements and challenges of culturing microorganisms in hydrogels versus mammalian systems and highlight recent breakthroughs in bacterial bioprinting that are advancing microbiological research, leading to current and emerging applications in areas including oral health. By synthesizing current knowledge and identifying promising future directions, this review underscores the potential of microbial hydrogel culture as a versatile platform for investigating microbial communities, probing bacterial–material interactions, and engineering living materials with applications in human health and environmental systems.