Background and aims <p>Modern agriculture requires smart and sustainable fertilization approaches. A strategy to delay the nitrification losses involves the use of nitrification inhibitors. Similarly, biostimulants may enhance nutrient uptake efficiency. This study aims to evaluate the potential synergistic effects of the 3,4-DMPP nitrification inhibitor (NI) and an <i>Ascophyllum nodosum</i>-based biostimulant (ANb) in mitigating nitrogen losses while maintaining the growth and physiological performance of tomato plants under low-nitrogen conditions.</p> Methods <p>Tomato (<i>Solanum lycopersicum</i> L.) plants were subjected to different levels of nitrogen regimes combined with NI and ANb applications. Physiological traits, yield, soil and leachate nitrogen dynamics were assessed. Untargeted metabolomics of leaves and roots was performed to elucidate treatment related metabolic reprogramming.</p> Results <p>Under nitrogen-limited conditions, the combined application of ANb and NI reduced NO₃⁻ in leached water by 48% compared to NI applied alone at 14&#xa0;days after the transplant. This combined treatment enhanced photosynthetic efficiency (Phi2), during both early and late development stages, increasing Phi2 values by 34.1% and 73.5%, respectively, compared to 0% N-fertilization treatment. Untargeted metabolomics pointed out distinct metabolomic reprogramming triggered by the combination of NI with ANb, with the most pronounced modulations detected in early-stage leaves, in a way related to abiotic stress resilience, defence mechanisms, and carbon–nitrogen balance. Moreover, the combination of NI and low nitrogen resulted in lower malondialdehyde (MDA) accumulation in harvested leaves.</p> Conclusions <p>Our findings confirm the impact of NI in low nitrogen conditions, while outlining the complementary and positive contribution of its combination with ANb.</p>