We present a novel absorption correction approach for elemental distribution images obtained with a laboratory confocal micro X-ray fluorescence spectrometer. The procedure is suited especially for biological samples, as a constant dark matrix with a varying minor or trace element distribution is assumed. The constant absorption in the sample is extracted from depth dependent measurements. By using the concept of an effective excitation energy, depth-dependent, and element-specific excitation energy values are calculated. For each voxel of a full 3D measurement, a correction is performed taking into account the actual number of voxels in the excitation and detection path. As proof of concept, the embryonic region of pearl millet seeds is investigated. Data are measured from the top and bottom side, resulting in a good agreement after the application of the absorption correction procedure. The distribution of elemental micronutrients is compared in seeds of two pearl millet genotypes. The corrected images illustrate different localization patterns of the micronutrient elements in pearl millet seed tissues.