Located within the Eastern High Atlas Mountain Range of Morocco, the Jbel Houanite mining district represents a polymetallic hydrothermal system with a structurally controlled genesis associated with a Paleozoic tectonic heritage followed by Atlasic reactivation. The results of the litho-structural studies suggest that mineralization is preferentially localized along E–W and NE–SW fault systems and subvertical foliation associated with inherited Hercynian shear zones. The occurrence of quartz stockwork veins and extensive fracturing suggests prolonged hydrothermal circulation through these highly permeable structural corridors. Geochemical data also reveal a distinction between a Fe-Zn sulfide assemblage typical of a volcano-sedimentary environment, and an Au–Sb–Ag–Pb assemblage related to a hydrothermal event associated with tectonic remobilization. Antimony was found to be the most reliable indicator element for gold mineralization. Hydrothermal alteration is dominated by phyllic assemblages characterized by enrichment in K–Rb–Cs and depletion in Ca, reflecting intense sericitization associated with fluid flow along deformation zones. Ag/Au ratios, together with the mineralogical and geochemical characteristics, suggest mesothermal to epithermal conditions and hydrothermal activity at intermediate crustal depths. Mineralogical mapping and trace-element analyses show that Au, As, Fe, and Sb are strongly spatially associated, with arsenopyrite and stibnite representing the principal As- and Sb-bearing sulfide phases associated with Au-bearing mineralized zones. No geochemical evidence for porphyry, volcanogenic massive sulfide (VMS), or Ni–Cu mineralization was identified, arguing against a direct magmatic or submarine volcanogenic origin and supporting a tectonically driven orogenic setting for the mineralization. The combined structural, mineralogical, and geochemical evidence indicates a polygenic mineralization process, with an early syngenetic sulfide phase followed by tectonically driven hydrothermal remobilization and concentration of Au within shear zones. There are also geological similarities between the Jbel Houanite mining district and major orogenic gold provinces within North Africa, and indicate how important inherited crustal structures are in determining the circulation of fluids and their mineralization.