Abstract Zn is the most deficient micronutrient in soils worldwide and the most important and limiting micronutrient essential for rice growth and yield. It can be applied in the soil for rice cultivation or by coating seeds or leaves of plants. However, only a small amount of Zn can be applied by coating seeds or plants. We evaluated the effect of dose, source and application time of zinc (Zn) on germination, cold test (germination), seed physiological potential and flooded rice yield. The rice cultivar was Puitá INTA Cl, and the laboratory experimental design was completely randomized with a factorial 6 × 2 scheme. Six Zn doses were assessed: 0, 50, 100, 200, 400 and 800 g ha −1 , using two Zn sources such as ZnSO 4 .7H 2 O and ZnCl 2 . After treating the seeds, germination, seedling length, seedling dry matter, cold test, accelerated ageing and seedling emergence were evaluated. Seven Zn doses were used in the field: 0, 50, 100, 200, 400, 800 and 1600 g ha −1 on seeds and at the V 4 and V 11 vegetative stages. The results showed that the Zn rice seed treatment did not change germination or seedling emergence. The seedling dry mass and germination at low temperatures (cold test) are the physiological potential parameters that benefited when using ZnSO 4 .7H 2 O. Foliar application of ZnCl 2 at the V 11 vegetative stage caused leaf damage when used at a dose of 400 g ha −1 , and caused more intense damage at 1600 g ha −1 . Treating rice seeds by coating with ZnCl 2 provided 6.4% higher grain yield compared to that of ZnSO 4 .7H 2 O. Applying Zn by coating the seeds promoted 5.8% higher rice grain yield and increased grain yield 7.0% by spraying at the V 11 stage compared with that at the V 4 vegetative stage. The principal components analysis by seed treatment condition showed that the cold test and accelerated ageing had the highest contributions to the first and third components and acted in opposition to grain yield. Yield had the highest contribution to the second component and was the third component that most influenced the first and third components