In this research, the effect of soil application of three different sources of zinc (Zn) fertilizers including nano Zn chelate, Zn sulfate and nano Zn oxide (ZnO) each at three levels of 0, 250 and 500 mg kg−1 was examined in a 12-year-old vineyard. The results of the soil incubation test of different Zn containing fertilizers (with equal amounts of Zn) showed that these compounds had the highest availability during the first week they are added to soil, but over time this availability reduced. The highest Zn availability was related to nano Zn chelate and the lowest availability was related to nano ZnO and control treatments. Moreover, the amount of Zn extracted at the end of the growing season was lower in nano Zn chelate- treated soils than those treated with Zn sulfate and nano ZnO. The highest yield was related to those vines treated with nano Zn chelate at 500 mg kg−1 and the lowest was observed in control vines. Also, the highest and lowest total phenol and soluble sugars was detected in 500 mg kg−1 nano Zn chelate- treated and control vines, respectively. Berry anthocyanin, flavonoid, titratable acid, catalase, and guaiacol peroxidase activity, protein, ascorbic acid, iron, and potassium dramatically increased in response to nano Zn chelate application. For this reason, because nano Zn chelate is less stabilized on soil, it is better to use nano Zn chelate fertilizer instead of other Zn compounds for improving the yield and quality of grape berries, especially in calcareous soils.