Being at the interface of the geosphere, the biosphere, and the atmosphere makes the soil a particularly challenging object. Nevertheless, the importance of ecological and environmental aspects related to soils should encourage soil scientists to make use of new technologies, like 3D printing, to improve their comprehension of the soil. With 3D printing, parts are built up by adding materials layer-by-layer based on a three-dimensional model, producing almost any geometrically complex shape or feature in a wide range of materials. Here we present the major challenges and opportunities of 3D printing to connect the choice of the different technologies and the research challenges of soil science. For this purpose, a literature review was performed, and the related sources were classified in three main groups: the manufacturing of agricultural machinery and soil-science laboratory equipment and devices, the development of new materials as a basis for construction, and the study of the soil structure, behavior, and composition. The advantages, opportunities, and limitations of 3D printing in each research axis, as well as the potential applications of its technologies, are discussed. We show that despite the remarkable achievements in 3D printing development during the past few years, it is still under-used in the field of soil science. Beside the 3D printing applications considering the soil as a source of mineral raw materials, or as the basis for the development of technical infrastructures, new researches highlight the functioning of the soil itself as an ecological compartment. Indeed, one of the most important challenges for the application of 3D printing in this area is the accurate modeling and replication of the soil structure and composition. This challenge requires 3D-printed objects to be made of biocompatible yet chemically and mechanically stable materials manufactured under controlled conditions, which can mimic the many interactions occurring at this scale. Having 3D-printed soil models with strict and controlled composition and structure could help academics and researchers to conduct reproducible experiments and gain a better understanding of the parameters controlling soil ecology and functioning. This opens a new way to a broader utilization of 3D printing in soil science in the near future.