The distribution of volcanogenic massive sulfide (VMS), porphyry-epithermal, Alaska-type ultramafic-mafic complexes, intrusion-related Au, and granitoid Sn-W ore deposits in southwest Alaska supports current metallogenic models linking the formation of these deposit types to the emplacement of different suites of igneous rocks during the evolution of this convergent plate margin. Regional-scale aeromagnetic data provide a continuous set of observations over the deposits and show contrasting patterns over the igneous rock suites hosting the various deposit types. Combined with surface geologic data and regional metallogenic constraints, aeromagnetic data—filtered to enhance the anomalous magnetic field and map magnetic domains—were used to produce a mineral potential map across this accreted island-arc setting. The reduced-to-pole, upward continuation, and total horizontal gradient transform maps show anomalies that could represent porphyry-epithermal deposits within the intraoceanic- and continental-arc terranes. The tilt derivative transform highlights lineaments within the back arc that may represent zones with potential for VMS deposits. The truncations of tilt derivative lineaments outline a major magnetic domain boundary between the back-arc and craton margin, which is prospective for granitoid Sn-W deposits. Annular tilt derivative highs outline granitoids that could be associated with intrusion-related Au deposits within the craton margin. Shallow, magnetite-rich Alaska-type ultramafic-mafic complexes are mapped by their short-wavelength, high-amplitude anomalies. Successful mineral potential mapping across southwestern Alaska as performed in the present study suggests that filtered aeromagnetic data can be effectively used in mineral exploration in convergent continental margin settings.