Purpose <p>Quince A (<i>Cydonia oblonga</i> Mill.) as a dwarfing rootstock is commonly used in pear cultivation. In calcareous soils, pear cultivar ‘Huangguan’ (<i>Pyrus bretschneideri</i> Rehd.) grafted onto quince A (HQA) is susceptible to Fe deficiency, whereas ‘Huangguan’ grafted onto <i>Pyrus betulifolia</i> Bunge (HPB) is not. We assumed that bicarbonate restricted the processes of Fe uptake or utilization in HQA compared with HPB.</p> Methods <p>Three treatments [pH6.3 as the acid growth condition, pH8.3 as alkali growth condition and B-pH8.3 as alkali-biocarbonate growth condition (adjusted by bicarbonate)] were tested, and some parameters of Fe uptake and utilization in two rootstock-scion combinations were analysed.</p> Results <p>Leaf Fe deficiency chlorosis in the two combinations only occurred in B-pH8.3, with HQA being more severely affected than HPB. In both HPB and HQA, root Fe uptake in B-pH8.3 was the lowest among the three treatments. In both HPB and HQA, inactivation of Fe in leaves was more severe at B-pH8.3 than pH6.3 and pH8.3 associated with the high apoplastic pH and low ferric chelate reductase (FCR) activity at B-pH8.3. However, at B-pH8.3, HPB had higher leaf FCR activity and leaf apoplastic Fe concentration than HQA.</p> Conclusions <p>Bicarbonate not only decreased root Fe uptake but also restricted the Fe unloading and transfer processes in leaves. The capacity of HPB to unload Fe in leaves was stronger than that of HQA when grown in the medium containing bicarbonate. These findings explain the more severe chlorosis in HQA than HPB when grown in calcareous soils.</p>