Purpose The biological pest control efficiency of entomopathogenic fungi is improved by the endophytic establishment and combination with agricultural recommended pesticides and plant extracts. This study aimed to evaluate the effects of B. bassiana and M. anisopliae on biological control of T. vaporariorum, endophytic colonization, and compatibility with selected pesticides. Methods The endophytic colonization ability of entomopathogenic fungal isolates was evaluated by using soil drenching and foliar spraying methods under greenhouse condition. Compatibility interaction of potential entomopathogenic fungi with selected pesticides was calculated based on the biological index formula. Results The endophytic colonization pattern of B. bassiana and M. anisopliae isolates using soil drench and foliar spray inoculation methods exhibited significant differences in the different parts of tomato plants. The endophytic B. bassiana and M. anisopliae isolates induced a significant reduction in the number of nymphs and adults of T. vaporariorum (p < 0.001). Thus, the application of B. bassiana AAUMB-29 reduced nymphs by 67% while M. anisopliae AAUDM-43 reduced adults with a percentage reduction of 52% over control. The compatibility study revealed that all tested concentrations of neem extract and chemical pesticides were caused by different levels of inhibition on vegetative growth, germination, and sporulation of M. anisopliae AAUDM-43, B. bassiana AAUMFB-77, and B.bassiana AAUMB-29. The biological index vales indicated that all isolates were compatible with neem oil, neem seed crud extract, and chemical insecticides at both half and recommended doses. Conclusion The tomato endophytic B. bassiana AAUMB-29 and M. anisopliae AAUDM-43 were convinced significant reduction of T. vaporariorum, and highly compatible with selected pesticides. These potential isolates should be used in integrated pest management programs