Cedrus deodara is the central conifer plant affected by ozone and nitrogen pollutants among forest species worldwide. The growth of C. deodara depends upon the ectomycorrhizal (ECM) association, which is usually disturbed by these factors. This study aims to understand how these factors affect plants at physiological and biochemical levels. Three fungal strain consortiums were inoculated with two-year-old C. deodara seedlings. The stresses of 100 kg N h−1and 100 ppb O3 were applied for six months to study their impact on chlorophyll and antioxidant enzymes (SOD, CAT, and APX). The results showed that C2 (Consortium of Cedrus deodara) positively impacted the growth of selected plant species. The high photosynthesis rate was determined by enhanced chlorophyll content, and C2-treated plants showed high chlorophyll content. Relatively, chlorophyll a and b contents increased significantly in the seedlings treated with Ethylenediurea (EDU) alone and with ozone stress. In addition, a significant difference was observed between EDU and O3-treated plants (14% EDU400-O3 and 23% EDU600-O3) and the control. Overall, antioxidant activities were higher in the treated samples than in the control. The order of SOD activity was C2 (448 U/gFW) and lowest (354.7 U/gFW) in control. APX also showed higher activity in treated plants in C1 ≥ C2 ≥ C3+O3, whereas CAT activity was the highest in C2 treatments. Ozone and nitrogen-stressed plants showed higher activities than EDU-treated plants compared to non-treated ones. Our findings highlight the importance of understanding the signaling effects of numerous precursors. Moreover, an extended investigation of seedlings developing into trees must be conducted to verify the potential of ectomycorrhizal strains associated with C. deodara and comprehend EDU's role as a direct molecular scavenger of reactive toxicants.