Somatic embryogenesis is an important biological process in several plant species, including sugar cane. Proteomics approaches have shown that H pumps are differentially regulated during somatic embryogenesis; however, the relationship between H flux and embryogenic competence is still unclear. This work aimed to elucidate the association between extracellular H flux and somatic embryo maturation in sugar cane. We performed a microsomal proteomics analysis and analyzed changes in extracellular H-flux and H-pump (P-H-ATPase, V-H-ATPase, and H-PPase) activity in embryogenic and non-embryogenic callus. A total of 657 proteins were identified, 16 of which were H pumps. We observed that P-H-ATPase and H-PPase were more abundant in embryogenic callus. Compared to non-embryogenic callus, embryogenic callus showed higher H influx, especially on maturation day 14, as well as higher H-pump activity (mainly, P-H-ATPase and H-PPase activity). H-PPase appears to be the major H pump in embryogenic callus during somatic embryo formation, functioning in both vacuole acidification and PPi homeostasis. These results provide evidence for an association between higher H-pump protein abundance and, consequently, higher H flux and embryogenic competence acquisition in the callus of sugar cane, allowing for the optimization of the somatic embryo conversion process by modulating the activities of these H pumps.