The term endophyte refers to a group of microbes that inhabit plant internal tissues such as bacteria and fungi. In this study, we isolated Beauveria sp. AUMC 15401 from the internal tissues of tomato leaves and extracted the alkaloidal contents from the leaves. Also, gas chromatography–mass spectrometry (GC–MS) analysis was used to identify the composition of the alkaloidal extract. The analysis showed that Beauveria sp. AUMC 15401 colonization stimulates plant secondary metabolism to produce novel alkaloids compared with the control tomato extract. Furthermore, the alkaloidal extract from the infected tomato leaves showed a high cytotoxic effect against A549 adenocarcinoma human alveolar basal epithelial cells. In addition, molecular docking studies were performed to investigate the potential binding of each alkaloid in the extract with epidermal growth factor receptor, vascular endothelial growth factor receptor 2, and SRC tyrosine kinases. These proteins are the main key factors in epithelial malignancies and their inhibition could reduce tumor growth. A pharmacokinetic study (absorption, distribution, metabolism, and excretion) was also conducted to determine the potential of the isolated alkaloids to be oral active candidates.