Improving nitrogen use efficiency (NUE) is critical to advancing sustainable cereal production, particularly under Mediterranean conditions where environmental pressures challenge input-intensive practises. This study evaluates NUE in Tritordeum, a climate-resilient wheat–barley hybrid, using a holistic experimental approach that integrates pre- and post-harvest soil analyses, including an electrical conductivity (EC) assessment, plant and seed nutrient profiling, and an evaluation of yield performance and nitrogen ratio dynamics. Four treatments were tested: conventional urea (T1), urea with an urease inhibitor (NBPT) (T2), urea with a nitrification inhibitor (DCD) (T3), and an unfertilised control (C). While conventional urea achieved the highest yield (1366 kg ha⁻¹), enhanced-efficiency fertilisers (EEFs) improved nutrient synchronisation and seed nutritional quality. Specifically, EEFs increased seed zinc (T2: 34.93 mg/kg), iron (T1: 33.77 mg/kg), and plant potassium (T2: 1.66%; T3: 1.61%) content, and also improved nitrogen remobilisation (elevated Nplant/Nseed ratios). EEFs also influenced soil properties, increasing organic matter (T3: 2.75%) and EC (T3: 290.78 μS/cm). These findings suggest that while EEFs may not always boost yield in the short term, they contribute to long-term soil fertility and nutrient density in grain. This study underscores the importance of synchronising nitrogen availability with Tritordeum’s phenological stages and highlights the crop’s suitability for sustainable, low-input agriculture under climate variability.