Updated project metadata. Sugarcane (Saccharum spp.) is one of the most important crops for sugar, biofuels and bioenergy production, becoming an important commodity in the world agricultural market for more than 100 countries. In this study, label-free quantitative proteomics and phosphoproteomics analyses were performed to investigate signaling events related to somatic embryo maturation and differentiation in sugarcane. Embryogenic callus (EC) at the multiplication (EC0) and after 14 days (EC14) under maturation were compared. A total of 251 phosphoproteins and 700 proteins were differentially regulated and accumulated, respectively, in the EC14/EC0 comparison. Metabolic pathways analysis showed that proteins and phosphoproteins are enriched in lysine degradation and starch/sucrose metabolism during multiplication, while differentiation of somatic embryo involves the regulation of energetic metabolism, including TCA cycle, oxidative phosphorylation, and carbon metabolism. Multiplication-related phosphoproteins were mainly associated to abscisic acid responses and transcriptional regulation comprising the TOPLESS (TPL), SNF1 kinase homolog 10 (KIN10), SEUSS (SEU), and LEUNIG_HOMOLOG (LUH) proteins. In maturation-related phosphoproteins, the phosphorylation of the proteins light harvesting complex photosystem ii, CURVATURE THYLAKOID 1B, vacuolar proton ATPase A1 and phytochrome interacting factor 3-LIKE 5 is associated to bioenergetic metabolism and carbon fixation. Motif analysis revealed 15 phosphorylation motifs, of which the [D-pS / T-x-D] motif was unique for the phosphopeptides identified during somatic embryo differentiation. Co-expression network analysis of proteins and phosphoproteins revealed the interaction between SNF1-related protein kinase 2 (SnRK2), abscisic acid responsive elements-binding factor 2 (ABF2), and KIN10, indicating the role of these proteins in the embryogenic competence in EC0. The interactions between ubiquitin-conjugating enzyme 5, ubiquitin-conjugating enzyme 35, small ubiquitin-like modifier 1, and histone deacetylase 1 may be involved in post-translational protein modification during the embryo maturation stage. argonaute 1 (AGO1) also interacts with POLTERGEIST (POL) and may integrate gene silencing and regulation of meristem identity during somatic embryo development. These results reveal novel dynamics of protein regulation in somatic embryogenesis and identify new potential players in somatic embryo differentiation and their phosphosites.