Incorporating bio-fertilizers, such as arbuscular mycorrhizal fungi (AMF), into mixed cropping systems has emerged as an innovative and sustainable approach to enhance crop growth and promote sustainable production. The study was conducted in two distinct locations within a mixed cropping system of corn and quinoa. Phosphorus fertilizer was applied at three different levels 50, 100, and 150 kg/ha while also considering the presence or absence of mycorrhiza. Cropping ratios included individual cultivation of quinoa, maize, and intercrop ratios of 50: 50, 75: 25, and 25: 75 (maize: quinoa). The utilization of phosphorus fertilizer improved the symbiotic interaction between plants and arbuscular mycorrhizal fungi, resulting in an increased rate of inoculation by AMF. The 50: 50 intercropping ratio, combined with the application of AMF, resulted in the highest contents of flavonoids, total phenolic compounds, tannins, saponin, antioxidant activity, and phytic acid in quinoa. Our findings demonstrated that AMF exhibit specific roles in optimizing plant strategies for phosphorus uptake and the efficient utilization of phosphorus in the mixed cropping. Recommending the application of AMF in a 50:50 intercropping ratio could be proposed to farmers as a friendly method to attain favorable phytochemical characteristics, particularly when using 50 kg/ha of phosphorus fertilizer.