Mosquito control in Egypt depends on applying chemical synthetic pesticides that impact negatively on human health and the environment as well as the development of antibiotic and chemical resistance. This study aims to control the 3rd and 4th instars of Culex pipiens larvae using four bacterial strains. According to Phenotypic and molecular identification, the four isolates were identified as Bacillus subtilis MICUL D2023, Serratia marcescens MICUL A2023, Streptomyces albus LARVICID, and Pseudomonas fluorescens MICUL B2023. All strains were deposited in GenBank under accession numbers OQ764791, OQ729954, OQ726575, and OQ891356, respectively. Larvicidal activity of all microbial strain metabolites against a field strain of C. pipiens explored low LC50 results and reached its lowest values on the 3rd day with values of 6.40%, 38.4%, and 46.33% for P. fluorescens, S. albus, and S. marcescens, respectively. In addition, metabolites of P. fluorescence were more toxic than those of S. albus, followed by S. marcescens. B. subtilis shows no larvicidal effect on both field and lab mosquito strains. Microscopic alterations of 3rd and 4th instars showed toxic effects on different body parts (thorax, midgut, and anal gills), including losing external hairs, abdominal breakage, and larvae shrinkage, as well as different histological malformations in the digestive tract, midgut, and cortex. GC–MS analysis detected 51, 30, and 32 different active compounds from S. albus, S. marcescens, and P. fluorescens, respectively. GC detected 1, 2-BENZEA2:A52NEDICARBOXYLIC ACID, 2-Cyclohexene-1-carboxylic-acid-5-2-butenyl-methyl ester, and 3 octadecahydro2R3S4Z9Z-11R-12S from S. albus, S. marcesens, and P. fluorescens, respectively. Total protein, Total carbohydrate, and Acetylcholine esterase activity indicated significantly low levels on the 3rd day. All strain metabolites were safe against HSF cell lines. The docking results confirmed the role of the produced metabolites as larvicidal agents and Acetylcholine esterase inhibition. Such a problem need more studies on applying more and more natural pesticides.