We present in situ microanalyses of Fe3+/ΣFe in mantle-derived kaersutites as measured by electron probe microanalysis (EMP) based on the “self absorption induced FeLα peak shift” method. The EMP results are not in agreement with bulk (wet chemistry) data. The heterogeneities revealed for some kaersutite megacrysts, when comparing bulk and EMP Fe3+/ΣFe results, cannot explain the differences with the EMP measurements. It is thus proposed that any EMP overestimation of Fe3+/ΣFe results from a beam-induced dehydrogenation and a subsequent oxidation of Fe2+ to Fe3+ according to the known relation: Fe2+ + OH− = Fe3+ + O2− + 1/2 H2. To demonstrate this phenomenon, H losses were measured by secondary ion mass spectrometry (SIMS) after EMP irradiation at different beam currents on two amphiboles with 1.1 and 1.7 wt% H2O, respectively. In both amphiboles, H losses were observed under high beam currents (240 and 100 nA). No dehydrogenation is observed under lower beam currents for the 1.1 wt% H2O amphibole, but still occurs, down to at least 50 nA, for the amphibole with the greatest H2O contents. Amphiboles with low H2O contents (below ~0.5 H+) are less affected by beam damage. For amphiboles with higher H2O contents, the electron beam current density should be reduced with consideration given to the resulting high statistical errors.