A field experiment was conducted in a pomegranate (Punica granatum L.) orchard of the well-known cultivars Wonderful and Acco, located in the farm of Aristotle University. The trees were sprayed, every 15 days from flowering (April) to fruit maturation (September), with solutions containing 0, 25, 50, 100 μm Ni, and 100 μm Ni + 100 μm B prepared with Ni(NO3)2·6H2O and boric acid. Leaves and fully ripe fruits were initially sorted into cracked and uncracked ones, then further separated into peel and seeds, sampled, and analyzed. Nickel sprays were effective in controlling fruit splitting as well as Ca and Mg concentration of fruit peels. The correlation between cracking level and Ni concentration in solution was linear and negative. Cracking percentage with 50 μm Ni was lower in ‘Wonderful’, whereas no difference was recorded between the cultivars in the remaining treatments. Leaves had the smallest Ni concentration compared with fruit peel and seeds. Calcium concentration of pomegranate peels was higher than that of control peel at 50 μm Ni in ‘Wonderful’. Concerning ‘Acco’, the treatments 25 μm Ni, 50 μm Ni, and 100 μm Ni + 100 μm B reduced Ca concentration, compared with control. ‘Wonderful’ fruit peel contained more phenolics than ‘Acco’. The treatments 25, 50, and 100 μm Ni increased significantly the flavonoid concentration of fruit peels. The antioxidant capacity ferric-reducing antioxidant potential (FRAP) was linearly increased with Ni concentration in solution in ‘Wonderful’, whereas in ‘Acco’ it decreased at 25 and 50 μm Ni. Our data indicates that improving Ni nutrition of pomegranate can potentially reduce crop loss due to cracking and modified phenol and flavonoid concentration and FRAP value of fruit peel.