Purpose <p>This study evaluated the agronomic, physiological, and biochemical effects of nano zinc oxide (NZ) and nano silica (NS) on black cumin (<i>Nigella sativa</i> L.) across two growing seasons (2023 and 2024), focusing on crop performance and seed oil quality under sustainable fertilization practices.</p> Methods <p>A two-year field trial was conducted using a randomized complete block design with three replications. Treatments included foliar applications of NZ at 100, 150, and 300 mg L^− 1; NS at 100 and 200 mg L^− 1; a conventional NPK fertilizer; and an untreated control.</p> Results <p>NS100 and NZ300 significantly increased plant dry weight (28.9&#xa0;g and 27.8&#xa0;g, respectively) compared to NPK and control. NZ300 enhanced chlorophyll a (5.23 mg g^− 1 FW), chlorophyll b (2.5 mg g^− 1 FW), and antioxidant activity (DPPH: 89%), while NS200 showed the highest relative water content (RWC: 89%) and total phenolic content (1.24&#xa0;mg GAE g^− 1 DW). NS200 led to the greatest nitrogen (35.46 mg g^− 1) and phosphorus (12.18 mg g^− 1) accumulation, whereas NZ300 was most effective for zinc (7.33 mg g^− 1) and potassium (64.35 mg g^− 1) uptake. Photosynthetic efficiency was markedly improved under NZ300 and NS200, with photosynthetic rates reaching 29.73 and 26.3 µmol CO₂ m⁻² s⁻¹, respectively. Additionally, NS100 boosted polyunsaturated fatty acids (PUFA) to 57%, while NZ300 raised monounsaturated fatty acids (MUFA) to 26%.</p> Conclusions <p>Nano silica and nano zinc fertilizers significantly improved biomass accumulation, physiological traits, antioxidant capacity, mineral uptake, and seed oil quality in black cumin, outperforming conventional NPK treatments. These findings highlight the potential of nano-fertilizers as eco-efficient alternatives for enhancing the productivity and nutritional value of medicinal crops under field conditions.</p>