Biological nitrification inhibition (BNI) has already led to several studies mainly focused on underlying molecular mechanisms and applications to agriculture. We argue that it is also important to study BNI more systematically from the ecological and evolutionary points of view to understand its implications for plants and soil nitrifiers as well as its consequences for ecosystems. Therefore, we propose here a dedicated research agenda identifying the most critical research questions: (1) How is BNI distributed across plant phylogeny and why has it been selected? (2) What are the costs-to-benefits balance of producing BNI compounds and the relative impacts on BNI evolution? (3) Can we understand the evolutionary pressures leading to BNI and identify the environmental conditions favorable to BNI plants? (4) How has BNI coevolved with plant preference for ammonium vs. nitrate? (5) Diverse BNI compounds and various inhibition mechanisms have been described, but implications of this diversity are not understood. Does it allow inhibition of various groups of nitrifiers? (6) Does this diversity of BNI compounds increase the efficiency, spatial extension, and duration of BNI effect? (7) What are the impacts of BNI compounds on other soil functions? (8) Can field experiments, coupled to scanning of the diversity of BNI capabilities within plant communities, evaluate whether BNI influences plant-plant competition and plant coexistence? (9) Can field quantification of various nitrogen (N) fluxes assess whether BNI lead to more efficient N cycling with lower losses and hence increased primary production? (10) Can the impact of BNI on N budgets and climate (through its impact on N2O emissions and its indirect impact on carbon budget) be evaluated at the regional scale? We discuss why implementing this research program is crucial both for the sake of knowledge and to develop applications of BNI for agriculture.