3D bioprinting – the fabrication of geometrically complex 3D structures from biocompatible materials containing living cells using additive manufacturing technologies – is a rapidly developing research field with a broad range of potential applications in fundamental research, regenerative medicine and industry. Currently, research into 3D bioprinting is mostly focused on new therapeutic concepts for the treatment of injured or degenerative tissue by fabrication of functional tissue equivalents or disease models, utilizing mammalian cells. However, 3D bioprinting also has an enormous potential in biotechnology. Due to the defined spatial arrangement of biologically active (non-mammalian) cells in a biomaterial matrix, reaction compartments can be designed according to specific needs, or co-cultures of different cell types can be realized in a highly organized manner to exploit cell-cell interactions. Thus, 3D bioprinting technology can enable new biotechnological concepts, for example, by implementing perfusion systems while protecting shear sensitive cells or performing cascaded bioreactions. Here, we review the use of 3D bioprinting to manufacture defined 3D microenvironments for biotechnological applications using bacteria, fungi, microalgae, plant cells and co-cultures of different cell types. We discuss recent approaches to apply 3D bioprinting in biotechnological applications and – as it is a particular challenge – concepts for the real-time monitoring of the physiological state, growth and metabolic activity of the embedded cells in 3D bioprinted constructs. With these insights, we outline new applications of 3D bioprinting in biotechnology, engineered living materials and space research.