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Endophytic fungal isolates <i>Hypocrea lixii</i> F3ST1 and <i>Beauveria bassiana</i> G1LU3 were evaluated for their potential to endophytically colonize and induce active compounds in <i>Phaseolus vulgaris</i>, as a defense mechanism against pea leafminer (<i>Liriomyza huidobrensis</i>) and fall armyworm (<i>Spodoptera frugiperda</i>). Endophytic colonization was achieved through seed inoculation with the volatile emissions from <i>P. vulgaris</i> plants being analyzed using GC-MS. The crude extracts of <i>P. vulgaris</i> obtained using methanol and dichloromethane were assayed against leafminer and fall armyworm larvae using leaf dipping and topical application, respectively. The two isolates successfully colonized the entire host plant (roots, stems, and leaves) with significant variation (<i>p</i> < 0.001) between fungal isolates and the controls. The results showed qualitative differences in the volatile profiles between the control plants, endophytically colonized and insect-damaged plants attributed to fungal inoculation and leafminer damage. The crude methanol extracts significantly reduced the percentage pupation of 2nd instar leafminer larvae (<i>p</i> < 0.001) and adult-flies emergence (<i>p</i> < 0.05). The survival of the 1st instar fall armyworm larvae was also significantly reduced (<i>p</i> < 0.001) compared to the controls. This study demonstrated the high potential of endophytic fungi <i>H. lixii</i> and <i>B. bassiana</i> in inducing mainly specific defense compounds in the common bean <i>P. vulgaris</i> that can be used against pea leafminer and fall armyworm.