Natural products remain an important source of anticancer agents, yet identifying pharmacological vulnerabilities in chemotherapy-refractory tumors remains a major challenge. Natural terpenes (NT) represent one of the most structurally diverse classes of bioactive compounds, but their native scaffolds often display limited potency and restricted translational potential. Here, we applied a phenotype-driven screening strategy using a library of semi-synthetic terpene analogs to identify compounds capable of targeting therapy-resistant tumor states. A first-generation library of 137 semi-synthetic terpenoid analogues was functionally screened across 8 human tumor cell lines representing distinct tissue origins and biological phenotypes. Phenotype-oriented screening revealed that 58% of the library exhibited greater antiproliferative activity relative to their NT precursors, and 5 derivatives inducing >  90% growth inhibition. Functional prioritization identified TRX-41 as the lead cytotoxic compound, displaying low-micromolar potency, complete suppression of clonogenic survival, and rapid induction of cell death (90% within 10 h). In vivo toxicity evaluation in zebrafish embryos identified a measurable therapeutic window, exceeding by up to 44-fold the TRX-41 antiproliferative doses. Mechanistically, TRX-41 induced coordinated cell-cycle perturbation and apoptosis, accompanied by activation of death receptor–related signaling pathways, including TNF-associated programs. Importantly, the prioritized lead compound retained robust activity in breast cancer patient-derived organoids, with GR₅₀ values in the submicromolar range and preferential efficacy in aggressive and chemotherapy-refractory models. Collectively, these findings demonstrate that phenotype-driven pharmacological screening of semi-synthetic terpene libraries can identify therapeutically relevant pharmacological vulnerabilities in chemotherapy-refractory tumors. TRX-41 represents the first proof-of-concept lead compound emerging from this strategy and provides proof of concept for its application in the discovery of new anticancer agents active across biologically heterogeneous and chemotherapy-refractory tumors.