Twenty fungal endophytes were isolated from Nabq, and plug diffusion screening revealed four of those isolates to be promising. These isolates were identified molecularly as Aspergillus sp. of Sect. Flavi (ZSEFL2) and Sec. Niger (ZSEFL14), and Penicillium spp. closest related to Penicillum crustosum (ZSEFL15, 19). Investigations were conducted to determine the effects of culture parameters, such as the type of culture medium, incubation temperature, initial pH and agitation, on the production of antimicrobial metabolites in a culture filtrate extract. Using the disk diffusion technique, antimicrobial metabolite synthesis was evaluated. In comparison to the other three distinct culture media (PDB-y, rice, and Cz), PDB demonstrated to be the best culture medium for the four tested fungal endophytes, exhibiting high levels of the Antimicrobial Index (AI). Also, a restricted range of incubation temperatures resulted in the formation of bioactive metabolites, but raising the incubation temperatures from 25 to 30 °C increased the amount of bioactive metabolites produced. Moreover, the best initial hydrogen concentration typically ranged from pH 5 to 6. Finally, when the conditions changed from stationary to shaking, the bioactive secondary metabolite's antimicrobial efficacy reduced. The behavior of the four examined fungal isolates was consistent, and they all required the same conditions to produce the most bioactive metabolites. Moreover, ethyl acetate extract's MIC values against the investigated bacterial and fungal human pathogens ranged from 0.19 to 6.25 mg/mL.