The data reported here are associated with the article "Comparative phosphoproteome analysis upon ethylene and abscisic acid treatment in Glycine max leaves" [1]. Phosphorylation plays a critical role in the regulation of the biological activities of proteins. However, phosphorylation-mediated regulation of proteins and pathways involved in ethylene (ET) and abscisic acid (ABA) signaling is currently poorly understood. Therefore, we used a shotgun proteomics approach to identify the phosphopeptides and phosphoproteins in response to ET, ABA and combined ET+ABA treatments. Here, we present the Mass spectrometry, protein-protein interaction, Gene ontology and KEGG data associated with the ET and ABA signaling in soybean leaves [1].