Selective leaching of synthetic Mn and Fe oxide phases was examined using a Chemostat to control the system temperature, pH and reductant concentration or Eh. Reaction conditions for the selective dissolution of model phases of Mn oxide (birnessite, ‘MnO2’), amorphous Fe oxyhydroxide (ferrihydrite, Fe(OH)3.xH2O) and crystalline Fe oxide (hematite/goethite, Fe2O3/FeOOH) were examined, concomitant with the behaviour of dopant metals Cu, Pb and Zn, present at concentrations of 1000 mg kg−1 each. Part 1 of this study focused on achieving quantitative dissolutions of the target model phases within short reaction times (≤15 min) for the purpose of high-throughput field procedures. In this study, the behaviour of the doped trace metals during the selective extractions was examined. Selective extraction protocols were developed that attempt to optimize both the bulk phase dissolution and the selectivity of the doped trace metals hosted by particular phases. The behaviour of the doped trace metals suggests that trace metal selectivity is limited with respect to both re-adsorption onto and extraction from residual phases. Significant re-adsorption of extracted trace metals occurred under the necessarily milder conditions required for selective dissolution of Mn oxide (pH >3). At pH 5, 95% of Pb, 52% of Cu and 6% of Zn extracted from the Mn oxide phase re-adsorbed onto the residual amorphous Fe oxide phase. Partial extractions attempting to achieve selective dissolution of the Mn oxide phase and its associated trace metals must therefore be treated with caution. Selective extractions of soil samples from four different mineralized areas, employing the extraction conditions found to provide optimal selectivity, exhibited much slower dissolution kinetics for the bulk oxide phases, particularly for amorphous Fe oxide, in comparison to the model phases. Reaction times of ≤2 h are unlikely to be quantitative for amorphous Fe oxide extractions under these conditions; however, this leach is considered to be more robust than Mn oxide extractions.