A field experiment was conducted during the post-rainy seasons of 2020-21 and 2021-22 at the ICAR-Indian Institute of Millets Research, Hyderabad, using a split-plot design to evaluate the effects of boron (B) (0.5 %), zinc (Zn) (1 %) and their combination (B + Zn) applied through foliar sprays at panicle initiation (PI), 50 % flowering (FL), both stages (PI + FL) and as soil application (before sowing) on the growth, yield and seed quality of foxtail millet (cv. SiA 3156). Dual-stage foliar sprays of both B and Zn recorded maximum plant height (118 cm), productive tillers per plant (5), primary branches per panicle (119), panicle dry weight (10 g), seed yield per plot (1.40 kg), 100-seed weight (356 mg) and harvest index (48 %). The same treatment also produced superior seed quality traits with 100 % germination, 95 % field emergence and maximum seedling vigor indices indicating the synergistic effect of B and Zn. Foliar application treatments consistently outperformed soil application across both the years. Economic analysis indicated that foliar application of Zn (1 %) at both PI and FL stages recorded the highest benefit–cost ratio (1.6), while combined B (0.5 %) + Zn (1 %) application achieved the highest seed yield. The study highlighted that combining foliar applications of Zn and B at PI and FL significantly enhances plant growth, seed yield and physiological seed quality, underscoring its value as an efficient and sustainable seed production strategy in foxtail millet grown in micronutrient-deficient soils.