Microanalysis can provide rapid, quantitative characterization of mineral systems that complements the field- and core-scale observations traditionally made in ore deposits. We review recent innovations in microanalytical procedures and their application to studies of ore deposits. Case studies are presented examining how microanalysis can provide constraints on macroscopic processes within mineral systems. Synchrotron X-ray fluorescence shows centimetre-scale chemical variations associated with proximity to mineralization in samples from Sunrise Dam Gold Mine, Western Australia. Pseudomorphs of igneous plagioclase and chemically driven recrystallization interpreted from electron backscatter diffraction suggest that the system was dominated by fluid-driven brecciation with very little shearing. Both the fluid chemistry and fluid pressure evolved during a protracted sequence of vein formation and alteration accompanying gold mineralization. A second case study of sulphide mineralogy at the Mt Keith nickel sulphide deposit, Western Australia demonstrates how X-ray computed tomography combined with trace element mapping can constrain the chemistry and dynamics of magmatic systems. Large-scale interaction between silicate and sulphide melts, shown by homogenous palladium enrichment in pentlandite, leads to a large proportion of globular ores with a high nickel content. Increasing use of microanalysis in ore deposit geology is resulting in the constant reassessment of established models for ore genesis though a combination of micro- and macroscale datasets.