Aluminium (Al) stress is the second-leading abiotic stress on crops. An improved understanding of the response mechanisms of plants to Al stress will provide scientific guidance for enhancing the crops’ tolerance to Al stress. In this study, Al stress (50–200 μM AlCl3) caused visible damage to broad bean (Vicia faba L.) roots rather than shoots, which was attributed to Al accumulation and distribution in different tissues. Root transcriptomic analysis revealed that Al stress altered cell wall properties by downregulating lignin synthesis and several xyloglucan endotransglucosylase/hydrolase-, expansin- and peroxidase (POD)-encoding genes, which likely weakened cell extensibility to inhibit root growth. Additionally, Al stress impeded reactive oxygen species scavenging pathways involving POD activity and flavonoid biosynthesis, leading to oxidative damage characterised by malondialdehyde accumulation. These results indicate that optimising cell wall properties and/or enhancing antioxidant processes are crucial for alleviating Al toxicity to broad beans. Interestingly, exogenous application (500 and 1000 μM) of the flavonoid apigenin effectively alleviated Al toxicity in broad bean roots by partially improving the total antioxidant capacity of the roots. This study contributes to understanding the interaction between plants and Al and provides new strategies to alleviate Al toxicity in crops.