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Tomato (Solanum lycopersicum L.) is an important worldwide vegetable crop. This paramount crop would be infected by a serious set of pathogenic fungal diseases. Growth and production are hampered by early blight caused by Alternaria phragmospora. In vitro the production of growth promoted hormone indole acetic acid (IAA) by Aspergillus flavus isolated from the medicinal plant, Euphorbia geniculata was stimulated in culture media supplemented or not by tryptophan (120 and 40 μg mL−1) respectively. The blue fluorescence test showed that the endophytic A. flavus was lacking to produce aflatoxins. Inoculation of S. lycopersicum with A. flavus enhanced the fresh weight (FW) and plant length (PL) of S. lycopersicum significantly in comparison to untreated plants. The PL of treated plants was 39.05 cm ± 3.16, while control was 22.19 cm ± 4.54. IAA stimulated overproduction of lateral roots and root hairs in treated plants compared to control. After spraying with A. phragmospora , the treated plant with A. flavus showed healthy leaves and completely protected (100%) from the disease symptoms. There were significant increases in chlorophyll (1.68 mg g−1 FW), flavonoids (105.4 mg g−1 dry weight), carbohydrates (155.5 mg g−1 dry weight), phenolics (0.9 mg g−1 dry weight) and total proteins contents (94.13 mg g−1 dry weight) in treated plants relative to untreated control plants. Our findings demonstrated the contribution of A. flavus to improve the growth and the secondary metabolites contents of tomato, which subsequently leads to the improvement of the resistance of this plant to an aggressive plant pathogen like A. phragmospora. [ABSTRACT FROM AUTHOR]