To assess the potential role of polyembryonic rootstocks on tree growth, yield and physiology of five mango cultivars, a study was conducted during 2013–15 on seven-year-old grafted trees. Rootstock K-5 inhibited canopy volume (CV) of Pusa Arunima (70.54%), Pusa Surya (27.64%) and Dushehari (30.15%) as of trees on Olour, while it was Olour which had inhibitory effect on CV of Amrapali (33.19%) and Mallika (64.11%) as of trees on K-5 rootstock. Kurakkan rootstock promoted highest yield in Amrapali and Pusa Surya, while both Kurakkan and Olour for Pusa Arunima; and K-5 and Kurakkan for Mallika seem to be more productive. The highest total chlorophyll content in Pusa Surya, Mallika and Dushehari was recorded on Olour rootstock, while both Kurakkan and Olour tended to show its higher values in Pusa Arunima, but Amrapali trees had the highest total chlorophyll content on Kurakkan. Photosynthetic rate (A) was promoted by Olour in Pusa Surya and Pusa Arunima, while K-5 rootstock induced higher A in Amrapali and Dushehari. Similarly, transpiration rate (E) was increased by Olour in Pusa Arunima, Pusa Surya and Amrapali. Moreover, Pusa Arunima and Amrapali had the highest activity of superoxide dismutase (SOD) on Kurakkan, while for Pusa Surya and Dushehari, it was highest on K-5 rootstock. Significantly higher peroxidase (POX) activity in Amrapali and Mallika was observed on K-5 rootstock, while glutathione recuctase (GR) activity was found higher in Amrapali and Mallika on Olour. Furthermore, both Olour and Kurakkan effectively upregulated polyphenoloxidase (PPO) activity in Pusa Arunima, though it was higher in Pusa Surya on K-5 and Kurakkan rootstocks. Trees of Amrapali had higher PPO activity on Kurakkan rootstock but Olour was found more effective for Mallika. Total phenolic compounds were higher in Pusa Arunima and Amrapali on Olour rootstock but it was K-5 which promoted their higher accumulation in Pusa Surya and Dushehari. Based on our findings it could be inferred that rootstocks alter most of the physio-chemical parameters of scion cultivars in mango though the extent of regulation of activities was scion specific.