The polyadenylation factor EhCFIm25 has been recently reported as a biochemical target in Entamoeba histolytica. The prediction and experimental characterization of its interactome revealed close relationships between proteins involved in gene expression regulation and enzymes of energy metabolism. Here, the identification of the nuclear proteome of E. histolytica by mass spectrometry analysis showed the presence of typically cytoplasmic proteins in the nuclear compartment, which could have moonlight functions. Prediction of PPI network confirmed the relevance of some metabolic enzymes in the coordination between energy and RNA metabolism, opening new perspectives for human amoebiasis control.