The house flies Musca domestica )Diptera:musidae) are the primary carrier of many pathogens such as cholera, typhoid, anthrax, and others. The use of chemical pesticides as a basic method of control leads to many problems at the environmental and health level. The use of safe alternatives to chemical pesticides has become an urgent necessity. The research aims to find biological alternatives that are environment-friendly and non-pathogenic to humans in controlling house flies through the possibility of extracting and diagnosing some secondary metabolites produced by the fungus Metarhizium anisopliae and testing their effects on the second larval stage of house flies using different treatment methods that include direct spraying of the larvae, treating the food environment, and the dipping method. Secondary metabolites and toxins of Metarhizium anisopliae were extracted in liquid media PDB using a mixture of organic solvents such as ethyl acetate and methanol. The secondary metabolites were identified by gas chromatography-mass spectrometry (GC-MS). The results showed the identification of 10 chemical compounds, including phenol, 2,4-bis(1,1-dimethylethyl (C₁₄H₂₂O)., Diethyl Phthalate (C₁₂H₁₄O₄),  Hexadecanoic acid, methyl ester (C₁₇H₃₄O₂ ),  Phthalic acid, butyl undecyl ester (C₂₃H₃₆O₄) , 9,12-Octadecanoic (Z,Z )-, methyl ester ( C₁₉H₃₄O₂),  9-Octadecanoic acid, methyl ester, (C₁₉H₃₆O₂), 9,12,15-Octadecanoic acid,methyl ester,(Z,Z,Z) (C₁₉H₃₂O₂), Octadecanoic acid,methyl ester(C₁₉H₃₈O₂), Oleic Acid (C₂₄H₃₈O₄), 9-Octadecanoic acid (Z)-,2-hydroxyl (hydroxymethyl) ethyl ester(C₂₁H₄₀O₄) ,and Di-n-octyl phthalate (C₂₄H₃₈O₄ ). The results showed that the crude extract of the fungus cause the best mortality rate  in the second instar larvae at concentrations of 3 and 5% after 72 hours of treatment when  the mortality rates ranged between 60-100%. The mortality rates were directly proportional to the increase in concentration and time with a significant difference. The results also showed that the treatment of the food media was the most effective in affecting the larvae of flies, recording mortality rates that reached 100%, with a significant difference with direct spraying and dipping methods. These results reveal the significant efficacy of the tested secondary metabolite crude of m.anesopalae against Musca domestica which could be used as an ecofriendly alternative for insect control.