Early diagenesis of fossil plants, especially of their reproductive structures, provides essential information about the evolution of the group. In this study, we describe the morphology and early fossil diagenesis of isolated eudicot seeds collected in neosols (entisols) derived from limestones of Romualdo Formation, Araripe Basin, Brazil. They were studied using scanning electron microscopy, X-ray microtomography, and laser ablation inductively coupled plasma mass spectrometry in the imaging mode. The seeds were three-dimensionally preserved with volumes ranging from 10.16 to 18.57 mm3. The morphology and anatomy are described, and the specimens are identified as Fabidae seeds. It is known that Fabidae arose in the mid-late Cretaceous, so the seeds were considered diachronic to the paleobiota from the Romualdo Formation, not belonging to this stratigraphy. Based on the spectrometric intensities of the mapped elements, such as C, Fe, Si, and Cu, intensity images were elaborated on these elements on the surface and inside the seeds. The maps indicated higher intensities of C, Fe, Si, and Cu in the seed tissues than those in modern seeds, suggesting an early stage of diagenesis. The calcareous sandstones of the Romualdo Formation may have contributed charged ions carried by meteoric water and groundwater, and they later precipitated in the organic tissues, triggering the start of diagenesis in the soil.