The sunflower is the third most important source of edible oil and accounts for about 14% of world production of seed oils. Although the sunflower is well adapted to semi-arid regions, low soil fertility and nutrients deficiencies are important yield-limiting factors for sunflower production. The current experiment was carried out to study the effects of farmyard manure (zero (M1), 20 (M2) t ha−1) and nanostructured fertilizers (Mn, Fe, Zn ) on the agronomical traits, yield and yield components of the common sunflower (Helianthus annuus L.). The experiment was conducted during 2015–2016 growing seasons at a research field in Maragheh in the north-western part of Iran. Application of farmyard manure significantly improved such agronomic traits as plant height, leaf area, the number of leaves, the internode length, the stem diameter, the diameter of the branch head, the number of branches, the length of branches, achene length and achene width, the main capitulum diameter, 100-achene weight, oil content in an achene compared with non-manure condition. Results revealed that plants grown under M2 showed earlier flowering and possessed a higher chlorophyll concentration in leaves. Moreover, application of nano-chelated Zn and Fe considerably decreased the proportion of empty achenes and increased oil concentration, the achene yield and the harvest index. However, the best performance was obtained by combined application of nano-chelated Zn under manure conditions. The findings pointed to the importance of micronutrient deficiencies and balanced nutrition in this area. The overall results show that the integrated application of organic manure and nano-chelated micronutrients are more effective in improving the yield of sunflowers in semiarid production systems.