Background Endophytic fungi are excellent sources of new natural bioactive products with potential for exploitation in medical, agricultural, and industrial fields. Beneficial effects of endophytes are not only limited to promoting plant growth, but also to react as plant protection agents against phytopathogenic microorganisms and plant pests. The tomato leaf miner, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) is one of the main tomato pests in South America and in the Mediterranean basin. Results In the present work, the effectiveness of two endophytic fungi Clonostachys spp. and Beauveria bassiana were tested against T. absoluta larvae. Evaluation of the larvicidal effect in the laboratory by spraying 3 concentrations (D1 = 4 × 107 spores/ml, D2 = 4 × 106 spores/ml and D3 = 4 × 105 spores/ml) of fungal suspensions showed remarkable efficacy, which varied depending on the tested strain, concentration of application and time of exposure. Statistical analysis showed highly significant results on larval mortality rates for both endophytic than the control. After 15 days, dead larvae were mummified. Applications of tested isolates in greenhouse experiments confirmed their marked biological control efficacy than the synthetic insecticide (Emamectin benzoat). Number of mined leaves decreased depending on the contact time of the larvae with the fungal spores. Conclusion Results suggest that the two endophytic fungi B. bassiana and Clonostachys spp. were very effective entomopathogenic fungi against T. absoluta. Indeed, the present study revealed the pathogenicity of Clonostachys spp. against T. absoluta larvae for the first time.