Biomagnification of arsenic in food chain through wheat consumption poses a serious threat to human health. Therefore, it is necessary to elucidate mechanism of arsenic tolerance and detoxification in wheat. The study aimed to unravel the strategies adopted by arbuscular mycorrhizal fungi to alleviate arsenic toxicity in wheat. To accomplish this, independent and interactive effects of arsenic and Rhizophagus intraradices were assessed. Colonization by R. intraradices resulted in lower expression of high-affinity phosphate transporters (Phts) in comparison with non-mycorrhizal (NM) plants, thereby lowering arsenic concentrations in mycorrhizal (M) plants. Additionally, the subcellular fractionation analysis indicated differential distribution of arsenic. In NM plants, arsenic accumulated primarily in cell wall and organelle fractions. Conversely, in M plants arsenic was more concentrated in the cell wall and vacuolar fractions. This was related to higher levels of hydroxyl and aldehyde groups in cell wall fraction of root along with increased expression of C-type ATP-binding cassette transporters in root and leaves. These factors enabled effective sequestration of arsenic in the cell wall and vacuoles of M plants, thereby reducing its toxicity. Furthermore, the proportion of inorganic arsenic was lower in M plant, as it transformed it into less toxic organic forms.