Using bio-fertilizers such as arbuscular mycorrhizal fungi (AMF) in mixed cropping systems is a new sustainable method for improving crop growth and phytochemical product. Two location field experiments were performed to evaluate the effects of three levels of phosphorus fertilizer: control, 50 kg ha-1, and 100 kg ha-1, and Arbuscular mycorrhiza fungi at two levels: M1 (no mycorrhiza) and M2 (use of mycorrhiza) on total phenolic, tannin, flavonoids, saponin compounds, The amount of antioxidant enzymes (CAT, POX, SOD), and phytic acid of quinoa in intercropping with maize. Different cropping ratios included quinoa mono culture and replacement intercrop ratios of 50:50, 75:25, and 25:75 (maize: quinoa). The results showed the treatments used significantly affected the biochemical traits of tannin, saponin, total phenolic compounds, antioxidant activity, and phytic acid in quinoa. According to our results, the quinoa phytochemical traits were affected by experimental treatments and increased significantly in intercropping patterns after applying phosphorus fertilizer and AMF. The highest amounts of flavonoids (66.80 mggr-1), TPC (40.57 mggr-1), tannin (0.49 mggr-1), saponin (14.2 mg of saponin per gram of dry feed), antioxidant activity (79.85%), and phytic acid (3.8%) of quinoa were achieved in a 50:50 intercropping ratio by use of AMF. In general, use of AMF in a cropping ratio of 50/50 proposed to approach for phytochemical characteristics such as phenolic component and antioxidant activity and phytic acid and reducing harmful compounds such as saponin in quinoa under the use of 50 kg ha-1 phosphorus fertilizer.