The impact of rootstock on the pomological and biochemical characteristics of fruit has been investigated across various species of fruit-bearing trees. However, there are few reports on pomegranate. For this reason, an experiment was designed to examine the influence of rootstock on the pomological and biochemical traits of two distinct pomegranate cultivars, specifically ‘Rabab-e-Neyriz’ and ‘Khafr-e-Jahroom’. The design was completely randomized and encompassed two variables and five replications. Factor included two types of cultivars (‘Rabab-e-Neyriz’ and ‘Khafr-e-Jahroom’) and rootstocks in four kinds of cultivars (‘Post Ghermaz-e-Aliaghai’, ‘Gorj-e-Dadashi’, ‘Gorj-e-Shahvar’ and the control group with no grafting). In this study, both quantitative and qualitative parameters of the fruit especially the aril browning percentage included were evaluated. Based on results, the highest amount of aril anthocyanin, aril color, Titratable Acidity (TA), and Total Soluble Solids (TSS) in fruit juice, and also the highest seed width and peel thickness, as well as the minimal percentage of browning were identified in the fruits of ‘Rabab-e-Neyriz’ cultivar that were grafted onto the rootstock of ‘Post Ghermaz-e-Aliaghai’. The highest aril weight, seed thickness, seedlessness percentage, TSS/TA, and Vitamin C of fruit juice, along with the lowest TA and fruit peel thickness, were observed in the fruits of ‘Khafr-e-Jahroom’ cultivar grafted on ‘Gorj-e-Dadashi’ rootstock. The findings indicated that the interplay between scion and rootstock was significant in all traits. The findings indicated that the pomegranate fruit's biochemical and pomological traits were influenced by the rootstock type.