The vast consumption of nitrogen-based fertilizers is a significant source of environmental pollutants in all phases. While enhanced-efficiency nitrogen fertilizers (EENFs) improve N-use efficiency and reduce environmental impact, their performance depends on local conditions. Here, we present a relatively simple soil–fertilizer–plants greenhouse setup for the multi-phase tracking of N species of the effects of EENFs. We compared the environmental and agronomic performance of three urea-based EENFs (urea embedded with urease inhibitors, 2-month, and 4-month controlled release urea) and the common split surface application of the granulated urea. We tested the fertilizer applications on basil seedlings for three consecutive growing cycles. The analyses carried out included nitrogen recovery in plant biomass, soil, drainage, and NH3 and N2O emissions. This multi-phase research indicates that tested EENFs perform better than the standard surface-applied urea. The four-month controlled-release urea fertilizer matched the basil N demand the best, significantly increasing yield and improving nitrogen use efficiency while reducing NO3− leaching and NH3 and N2O emissions. The presented soil–fertilizer–plants experimental setup provides a relatively easy-to-handle system for the comprehensive tracking of N dynamics, including plant response. It allows stakeholders to estimate and improve fertilization sustainability.