In this paper, a detailed study of the influence of Mn2+ ions on quartz and hematite flotation (at pH 10.5 with starch/amine as depressor/collector) in the absence and presence of ethylenediaminetetraacetic acid (EDTA) is presented. By using zeta potential measurement and a careful analysis of manganese species present in water for dosages in which manganese hydroxide precipitated, we confirmed that the depression of both minerals by Mn2+ ions is due to the following: (i) the adsorption of Mn hydroxy complexes (Mn2(OH) 3+ and Mn(OH)+); (ii) Mn2+ and mainly (iii) the precipitation of Mn(OH)2 on mineral surfaces. These effects hindered the adsorption of amine species on the surfaces of the minerals (quartz and hematite). EDTA was used to complex Mn2+ to restore the recoveries of both minerals. This was confirmed by the species distribution diagrams of Mn and EDTA–Mn in water. Conditioning with starch followed by amine at pH 10.5 enabled a selective separation of these minerals.