A growing need exists to consider effects of biodiversity dynamics on the functioning of natural and anthropised ecosystems. This requires including the concepts of functional ecology, especially comparative trait-based ecology, in a broad range of theoretical and applied studies. In parallel, the importance of the belowground compartment is increasingly recognised, which has exponentially increased the number of studies that consider root functional traits, despite limited understanding of their meaning. This perspective article i) describes the origins of the trait-based ecology framework, ii) highlights current limitations of rootsystem studies, and iii) recommends ways to address these limitations. In recent years, studies claimed that aboveground functional ecology had theoretical foundations without adequate empirical support. Root functional ecology has experienced the same problems and, for several reasons, its foundations seem even more unstable. Firstly, roots are difficult to collect, and it is difficult to precisely define components of the root system that have homogenous functions. Secondly, root systems are complex organs and have a diversity of functions, such as taking up nutrients and water, storing resources, and anchoring plants. Thirdly, the theoretical background used in root functional ecology approaches is based on that of aboveground ecology, specifically leaf functional ecology. In the past several decades, root ecology benefitted from following in the footsteps of aboveground trait-based functional ecology, which highlighted the existence of a variety of trait spectra that were partially related to species' ecology or their interaction with symbiotic microorganisms. However, root functional ecology is currently at a crossroads and must move beyond this aboveground path and rediscover the origins of root ecology and include new traits based on root architecture and anatomy. Doing so requires developing innovative approaches that are more specific to the belowground compartment to improve understanding of plant roots and include them in large-scale studies.