Inappropriate soil management practices and specific climatic conditions in semi-arid region cause loss of soil organic matter (SOM), decline soil fertility, and trigger soil erosion processes and desertification. A two-year field study was carried out to investigate the effects of tillage intensity and fertilizer regime treatments on the productivity of sunflower (Helianthus annus L.) and soil physicochemical properties in the semi-arid highland region in northwest Iran (37 • 31 north (N), 46 • 53 east (E)). Five fertilizer treatments were included under conventional (CT) or reduced tillage systems (RT): F1, no fertilizer application; F2, 20 t·ha −1 farmyard manure (FYM); F3, 40 t·ha −1 FYM; F4: 20 t·ha −1 FYM + 50% of the recommended dose of nitrogen-phosphorus-potassium (NPK) chemical fertilizer; F5: full dose of the recommended chemical NPK fertilizer. Results showed that utilization of FYM decreased bulk density (BD); its effects were more evident under the highest SOM content for the F2 and F3 treatments, whereas application of mineral fertilizer had no significant effect upon SOM content, and elevated levels of FYM preserved higher organic carbon contents in topsoil. The highest N, P, and K contents of the soil were obtained with FYM plus inorganic fertilizer application in the RT system. Hydraulic conductivity and soil moisture content were significantly improved by RT and FYM application. The highest root growth was observed for F3 and F4 under the RT system. The effect of fertilizer and tillage treatments was more pronounced during the second year. Traits related to growth and seed quality such as achene oil content, leaf area, and harvest index were enhanced by chemical fertilization in the CT system. The highest achene yield and oil percentage were recorded for plants grown with F3 and F4. The best option for enhancing sunflower productivity and quality in semi-arid, high-altitude environments is the application of organic fertilizers amended with reduced amounts of chemical fertilizers.