The association of fine grained MgeNi silicates with oxy-hydroxides in laterites and saprolites represents challenges for ore processing, in particular, in nickel enrichment. The Weda Bay nickel deposit in Indonesia is a typical example of these complex ores, where clays such as nontronites develop on polyphase serpentinite as protolith. Thus, ores at Weda Bay have a very fine textured and complex mineralogy, which requires a comprehensive mineralogical identification through the use of a series of different types of analytical approaches (i.e. macroscopic and microscopic methods including SEM equipped with energy dispersive X-ray spectrometry (EDS), Raman spectroscopy, Infrared and X-ray fluorescence spectroscopy, and QEMSCAN® mapping). Nickel rich saprolites were found to be principally composed of several types of MgeNi serpentines, quartz, clays (nontronite in particular) and little amounts of iron hydroxides. Besides, some parts of the deposit were characterized by the development of nontronites at the interface between the saprolite and the limonite zone. Above this zone, the limonite zone is dominated by iron hydroxides as expected, which replace all earlier silicates including serpentine, and contains a significant amount of nickel. The representative composite ore sample contains several nickel bearers with variable nickel grade of 2 to 3%. Exceptionally richer phases such as polygonal Fe (Ni)-rich serpentine were also found with nickel grade of 5 to 10%. Serpentine types as well as other newly formed silicates such as Fe-Mg-(Ni) smectites, are intimately mixed, preventing any mineral separation. Therefore, the only phases which can be separated are quartz and magnetite. This complicates the upgrading of nickel in Weda Bay laterite ore.