The Ertsberg-Grasberg district hosts the world's largest Cu-Au(Mo) skarn system. The mineralization is related to the Pliocene Ertsberg- and Grasberg intrusive complexes, which intruded the Jurassic-Cretaceous Kembelangan Group siliciclastics and Cenozoic New Guinea Limestone Group. Despite previous studies, elemental migration across the porphyry-skarn system and across the different ore stages is still unclear. Here, we attempt to tackle this issue by integrating ore deposit geology, alteration/mineralization paragenesis, whole-rock geochemistry of the Ertsberg granitoids and carbonate wallrocks, together with spatial mapping of hydrothermal minerals and target/pathfinder trace elements at the Deep Mill Level Zone of Ertsberg. Ores at Ertsberg are mainly skarn-hosted, whose formation comprises five stages: (I) prograde skarn; (II) retrograde alteration; (III) massive anhydrite replacement; (IV) late hydrothermal veining; (V) supergene alteration. Massive magnetite and main CuAu mineralization occurred in Stage II and III, respectively, although minor Cu mineralization persisted to Stage IV.The Ertsberg granitoids have medium SiO2 and high Al2O3 contents, and consist mainly of (quartz-)monzonite and minor (monzo)diorite. Least-altered samples have upper crust-normalized enrichments in certain large ion lithophile elements (LILEs, e.g., U and K) and depletions in all high field strength elements (HFSEs, e.g., Ti, Y, and Yb). The samples are fresh to moderately-altered, featured by garnet-diopside skarn and/or porphyry-style (potassic, propylitic, phyllic) alterations and anhydrite replacement. Elemental mass balance calculation indicates that the porphyry-style alteration zones are featured by feldspar destruction and the accompanying alkali depletions, although the loss of KRb (in potassic and phyllic zones) and Ca-Ba-Sr (in propylitic zone) are balanced by their respective capturing in secondary K-feldspar-mica and actinolite-epidote-anhydrite. Decarbonation of the dolomitic wallrocks likely released Mg-Ca-Sr, which facilitated the subsequent forsterite-diopside exoskarn and anhydrite alteration. The enrichments of various ore-related target/pathfinder elements in these altered samples are consistent with their mineralized nature, e.g., FeMn (magnetite), Cu-Fe-Bi-Se-Te (bornite), MoRe (molybdenite), Au-Ag-As-Bi-Te (auriferous pyrite/arsenopyrite), Zn-Fe-Mn-Sn-In (sphalerite), and Pb-Ag-Bi (galena).Alteration mineral and target/pathfinder elemental distribution patterns show that the ore fluids were likely originated from the porphyry hydrothermal (potassic) centers near the Ertsberg pluton margin. The fluids then spread out from the potassic centers, forming the surrounding propylitic zone, and migrated along the largely NW-SE-oriented intrusive contact and fault zones. This formed the endoskarn in the Ertsberg pluton, the forsterite-diopside exoskarn in the Waripi Formation dolomite, and the garnet-diopside exoskarn in the Ekmai Formation limestone/calcareous sandstone-siltstone. As the hydrothermal system started to wane, the prograde skarn formation is partially overprinted/enveloped by retrograde serpentine and actinolite/tremolite-epidote-chlorite alterations, and then by magnetite mineralization and massive anhydrite replacement in the carbonate wallrocks. The texturally-destructive skarn formation, and the dissolution of carbonate wallrocks and hydrothermal anhydrite were likely pivotal in creating the highly-fractured Broken Zone, which served as a structural trap for the high-grade Cu-Au-Mo ore deposition.