Background and Aims <p>Intercropping is a sustainable agricultural system that provides numerous ecological benefits, including enhanced biodiversity, improved soil quality, and increased productivity. This study assessed the ecological advantages of intercropping Ajowan (<i>Trachyspermum ammi L.</i>) and Securigera ( <i>Securigera securidaca L.</i>) under various phosphorus fertilizer treatments and planting ratios.</p> Methods <p>A two-year field experiment (2021–2022) was conducted in Mamasani County, Iran, using a randomized complete block design with three replications. The treatments included five types of fertilizers: 100&#xa0;kg ha^− 1 of triple superphosphate (TSP), 50&#xa0;kg ha^− 1 of TSP with phosphate solubilizing bacteria (PSB), 50&#xa0;kg ha^− 1 of TSP with arbuscular mycorrhizal fungi (AMF), 50&#xa0;kg ha^− 1 of TSP with PSB + AMF, and a control. The intercropping ratios tested were 1:1 (A₁S₁), 1:2 (A₁S₂), 2:1 (A₂S₁), as well as sole cropping for each species. Measurements included root colonization, microbial respiration, phosphatase activity, seed yield, land equivalent ratio (LER) and phosphorus use efficiency (PUE).</p> Results <p>The results indicated that the combination of AMF + PSB with the 1:2 intercropping ratio resulted in the highest root colonization (70.7%), basal respiration (95.6&#xa0;mg CO₂ kg^− 1 day^− 1), and phosphatase activity (562.8&#xa0;µg PNP g^− 1 h^− 1). Although sole cropping with chemical fertilizer produced the highest seed yield for both species, the land equivalent ratio (LER) for the 1:1 and 1:2 intercropping systems was greater than 1 (1.13 and 1.17, respectively), indicating higher land use efficiency.</p> Conclusions <p>These findings underscore the effectiveness of integrated AMF + PSB applications in enhancing soil health, land productivity, and biodiversity in intercropping systems, presenting a sustainable strategy for the cultivation of medicinal plants. </p>