Glycogen Synthase Kinase-3 beta (GSK-3β) is a validated target-enzyme associated with Alzheimer’s Disease (AD). Usage of allosteric inhibitors of this enzyme represents a valid and promising therapeutic strategy due to their selective and subtle modulation, with a low probability of producing side effects. Nonetheless, only a few GSK-3β allosteric modulators with limited binding affinity have been uncovered so far and published in the public domain. Previous Virtual Screening (VS) studies have not considered such mechanism of action and did not achieve chemical diversity. Therefore, we applied two orthogonal VS workflows by means of shape-based similarity, QSAR, docking, and ADMET filters to select new and diverse GSK-3β allosteric inhibitors. Obtained hits have shown enhanced structural diversity and preliminary results as GSK-3β allosteric inhibitors according to in vitro assays. Furthermore, their GSK-3β allosteric inhibition were analyzed by blind docking and pocket coverage studies. These hits can be employed as template molecules for the discovery of more potent inhibitors, with the aim to expand the chemical space of GSK-3β allosteric modulators as promising agents in AD.