In this research, green synthesized magnesium oxide nanoparticles (MgO NPs) from lemon fruit extracts and their fungicidal potential was evaluated against Alternaria dauci infection on carrot (Daucus carota L.) under greenhouse conditions. The scanning and transmission electron microscopy (SEM and TEM) and ultra-violet (UV) visible spectroscopy were used to validate and characterize MgO NPs. The crystalline nature of MgONPs was determined using selected area electron diffraction (SAED). MgO NPs triggered substantial antifungal activity against A. dauci when exposed to 50 and 100 mg L⁻¹ concentrations but the higher antifungal potential was noticed in 100 mg L⁻¹ under in-vitro conditions. In fungal inoculated plants, a marked decrease in growth, photosynthetic pigments, and an increase in phenol, proline contents, and defense-related enzymes of carrot were seen over control (distilled water). However, foliar application of MgO NPs at 50 and 100 mg L⁻¹ resulted in significant improvement of plant growth, photosynthetic pigments, phenol and proline contents, and defense enzymes activity of carrots with and without A. dauci infection. Spraying of MgO NPs at 100 mg L⁻¹ had more plant length (17.11%), shoot dry weight (34.38%), plant fresh weight (20.46%), and root dry weight (49.09%) in carrots when challenged with A. dauci over inoculated control. The leaf blight indices and percent disease severity were also reduced in A. dauci inoculated plants when sprayed with MgO NPs. The non-bonding interactions of Alternaria genus protein with nanoparticles were studied using molecular docking.