Alternaria alternate YZM1 (OQ569158) causes Chia (Salvia hispanica L.) leaf spot was isolated and molecular identified from Fayoum governorate, Egypt. This study was conducted in Abshaway county, Fayoum governorate during the 2019/2020 and 2020/2021 seasons. Our goal was to control Alternaria leaf spot, also improve plant growth, seed quality and fixed oil productivity using organic inputs as alternatives to toxic chemicals used in fertilization and fungicides. Compost and biofertilizer species including Azospirillum brasilense, Bacillus megaterium var. phosphaticum and Bacillus circulans, were applied in both greenhouse and field experiments. Additionally, foliar spraying with biological control agents, including Trichoderma harzianum, Bacillus subtilis and Streptomyces rochei. Results indicated that, treatment with Trichoderma harzianum + Streptomyces rochei with biofertilizer led to the most significant reduction in disease incidence and severity (22.5% and 12.05% respectively). In addition, it significantly increased the activities of defense-related enzymes (peroxidase, polyphenoloxidase, and chitinase), total phenols, sugars and carbohydrates under greenhouse conditions. Furthermore, compost with biofertilizer increased plant height, spike number per plant, chlorophyll, plant NPK contents, seed yield per fed, fixed oil yield and seed quality under field conditions. According to our knowledge, this is the first report of Alternaria alternata causing Alternaria leaf spot on Chia in Egypt.