Water deficit stress can negatively affect oil quality, crop yields and soil infertility. Thus, we investigated the effects of rice-straw biochar, foliar silicon and their combination on quality, yield and physiological traits of sunflower grown under three water deficit stress treatments. Water stress treatments were 50% (WS0; no stress), 70% (WS1; moderate stress) and 90% (WS2; severe stress) depletion of the available soil moisture. The results showed that WS1 and WS2 negatively affected oil quality, mycorrhizal spores, yield and physiological traits of the sunflower; however, biochar, silicon and their combination significantly (p ≤ 0.05) improved most of those traits. Oil and oleic acid contents of sunflower grown under WS2 were decreased by 18% and 25.8% compared to those grown under WS0, respectively. Nevertheless, the biochar and silicon combination resulted in higher oil (10.2%) and oleic acid (12.2%) in plants grown under WS2 than those grown in untreated plots. Also, a significant increase (182% and 277%) in mycorrhizal spores was obtained in soil treated combination of biochar and silicon under WS1 and WS2 in comparison to untreated soil, respectively. On the other hand, plants grown under WS1 and WS2 exhibited reduced seed yield ha−1 by 16.5% and 53.5% compared to those grown under WS0, respectively. However, seed yield ha−1 were increased by 26.8% and 27.1% in plots treated with combined treatment compared to untreated plants, respectively. In addition, the biochar and silicon combination significantly increased stomatal conductance by 21.4% and 12.1%, reduced proline by 56.6% and 51.2% and reduced catalase activity by 13.4% and 17.3% under WS1 and WS2 compared to those grown in untreated plots, respectively. Therefore, the combined treatment of biochar and silicon can minimize and alleviate the negative effects of WS1 and WS2, improve oil quality, physiological traits, microbial activity and seed yield ha−1in sunflower plants.