The importance of engineers is increasingly recognized in soil science because of their implication in most important pedological processes. Furthermore, they contribute to ecological functions provided by soils in both natural and human-modified environments. In this review, we focus on the role of two ecosystem engineers: (1) plants, their root system, and associated microorganisms and (2) earthworms. First, we explain why they are considered as major soil engineers, and which variables (texture, porosity, nutrient, and moisture dynamics) control their activities in space and time (hotspots and hot moments). Then, their roles in three processes of soil formation are reviewed, namely, rock and mineral weathering, soil structure (formation, stabilization, and disintegration), and bioturbation. For each of them, the involved mechanisms that occur at different spatial scales (from local to landscape) are presented. On one hand, tree uprooting plays a key role in rock weathering and soil profile bioturbation. In addition, living and dead roots also contribute to rock alteration and aggregation. On the other hand, earthworms are mainly involved in the formation of aggregates and burrows through their bioturbation activities and to a less extent in weathering processes. The long-term effects of such mechanisms on soil heterogeneity, soil development, and pathways of pedogenesis are discussed. Finally, we show how these two main ecosystem engineers contribute to provisioning and regulating services. Through their physical activities of burrowing and soil aggregation, earthworms and plants increase plant productivity, water infiltration, and climate warming mitigation. They act as catalysts and provide, transform, and translocate organic matter and nutrients throughout the soil profile. Finally, due to inter- and intraspecific interactions and/or symbiosis with microorganisms (arbuscular fungi, bacteria), they enhance soil fertility, decrease parasitic action, and bioremediate some pollutants. Future research is, however, still needed for a better understanding of the relationships between adequate soil management, agricultural practices, and soil biota in a perspective of relevant maintenance and durability of ecological services.