The identification and accurate characterization of discrete grains of rare minerals in sulfide base-metal ores is usually a cumbersome procedure due to the small grain sizes (typically <10 μm) and complex mineral assemblages in the material. In this article, a new strategy for finding and identifying indium minerals, and quantifying their composition and abundance is presented, making use of mineral liberation analysis (MLA) and electron probe microanalysis (EPMA). The method was successfully applied to polymetallic massive sulfide ores from the Neves-Corvo deposit in Portugal. The presence of roquesite and sakuraiite could be systematically detected, their concentration quantified by MLA measurements, and their identity later confirmed by EPMA analyses. Based on these results, an almost complete indium deportment could be obtained for the studied samples. This validates the approach taken, combining automated mineralogy data with electron microprobe analysis. A similar approach could be used to find minerals of other common minor and trace elements in complex base-metal sulfide ores, for example Se, Ge, Sb, or Ag, thus permitting the targeted development of resource technologies suitable for by-product recovery.