The utilization of bio-fertilizers is a relatively new sustainable practice for improving growth and physiological characteristics in plants. 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 (mycorrhizal inoculation) on plant height, yield, Total Dry Weight, Leaf Area Index, Crop Growth Rate and Net Assimilation Rate, chlorophyll a, b, and total chlorophyll of quinoa and maize in intercropping system. Different cropping patterns were included quinoa and maize sole culture and replacement intercrop ratios of 50:50, 75:25, and 25:75 (Maize/Quinoa). The results showed that growth indices, chlorophyll a, chlorophyll b, total chlorophyll, and biological yield of maize and quinoa were significantly affected by studied treatments. The highest amounts of chlorophyll a (2.205/4.74 mg g-1 FW in maize/quinoa) and chlorophyll b (0.75/2.88 mg g-1 FW in maize/quinoa were achieved in a 50:50 cropping ratio, use of AMF and 50 kg ha-1 phosphorus fertilizer. Generally; AMF application in a cropping ratio of 50:50 may be proposed to farmers as an eco-friendly approach to achieving desirable physiological characteristics such as plant height, Plant dry matter, Yield, and chlorophyll, in quinoa under the use of 50 kg ha-1 phosphorus fertilizer. The highest growth indices, chlorophyll a, chlorophyll b, total chlorophyll and biological yield of maize were obtained by the 75:25 ratio. For the quinoa and the highest chlorophyll b and total chlorophyll were obtained by the 50:50 ratio.