One of Egypt’s most notable and historically significant vegetable crops is the Liliaceae plant, Allium cepa L. In this study, the effectiveness of methanolic extracts of Artemisia absinthium leaves, Calotropis procera latex, Moringa oleifera seeds, and Syzygium aromaticum clove was investigated in vitro and, in a greenhouse, setting against Fusarium oxysporum, the pathogen that causes onion basal rot in Assiut Governorate, Egypt. The S. aromaticum extract exhibited the inhibition peak (63.3%), whereas the A. absinthium extract had the lowest inhibition impact against F. oxysporum growth (41.1%). The gas chromatography-mass spectroscopy (GC–MS) analysis revealed that 82 important compounds, with abundances ranging from low to high, were present in the tested S. aromaticum’s methanolic extract. The primary components were acetaldehyde, hydroxy- and 2-propanone, 1,1,3,3-tetrachloro-(42.71%), 1,2-ethanediol, and methyl alcohol (34.01%). In comparison to the infected control, the disease severity was significantly reduced by 20% with the use of a plant extracts mixture and Dovex 50% and increased by 62.22% with the use of an extract from A. absinthium. When compared to the infected control, onion plant fresh weight and dry weight were considerably higher under the clove extract therapy. The plant extracts used in this study’s testing contain a number of active ingredients, including amino acids, vitamins, minerals, antioxidants, and enzymes, which is probably why they have such positive impacts. The application of a combination of plant extracts was suggested as a feasible strategy for improving the growth and productivity of onion plants by the study’s findings. More research is needed to comprehend the mechanisms by which plant extracts promote plant development and to optimize the concentration and timing of administration.