The traditional techniques employed for embedding plant samples are not suitable for the proper processing of small seeds with hard seed coats. Usually, these seeds are broken off from blocks during microtomy, which limits the technical success of this procedure. In this study, Melastomataceae seeds of 101 species were treated prior to embedding in historesin according to three treatments: (1) control, using the standard procedure; (2) fixation and subsequent softening with Franklin solution, glycerin and heating in a water bath; and (3) softening with Franklin solution and subsequent fixation (glycerin and heating in a water bath were also included). For Melastomataceae species, the second treatment provides the best results, and we were able to produce very good sections of the entire seed. Small hard seeds, similar to those found in Melastomataceae, are better embedded when they are softened after subjected to fixation. A combination of softening techniques is necessary to improve the embedding process and to obtain high-quality sections of the embedded samples. In this study, we established a practical, slightly toxic and inexpensive methodology to ensure good preparations for light microscopy that can be applied to a wide range of subjects related to seed science.