Glioblastoma is the most common and malignant primary brain tumor in adults, with current treatment presenting limited effectiveness. Resistance to therapy is consequence of the high molecular and cellular heterogeneity. Multitarget small molecules (MSMs) are emerging as a novel therapeutic strategy for the treatment of complex diseases such as cancer. In the present work, we have generated a novel family of indole-based MSMs designed to inhibit monoamine oxidases (MAOs), cholinesterases (ChEs) and histone deacetylases (HDACs), while acting as histamine H3 receptor (H3R) antagonists and sigma 1 receptor (S1R) agonists. For this, selected pharmacophoric moieties of the parent compounds Contilisant and HDAC inhibitor Belinostat were juxtaposed. 9 MSMs were synthesized and most of them exerted cytotoxic effect on glioma cells. Among them, 3 molecules were selected (MTP142, MTP156 and MTP150), and additional experiments revealed that they inhibited glioma stem cell (GSCs) activity, did not present toxicity and are expected to cross the BBB. In vivo and Omic studies were performed with MTP150 molecule, and results showed that it significantly reduced tumor growth in vivo, both alone and in combination with temozolomide (TMZ). Finally, transcriptomic and proteomic analyses on patient-derived GSCs revealed a deregulation in cell cycle and neurotransmission activity by the treatment with MTP150. In conclusion, our data reveal the efficacy of a novel family of MSMs in the pre-clinical setting of glioblastoma.