Tissue culture through somatic embryogenesis is the best method to produce the true-to-type of an elite oil palm plantlet. However, the mechanism underlying this process in oil palm is still unknown. We aimed to identify differentially expressed proteins during oil palm somatic embryogenesis using embryogenic callus, somatic embryo maturation and plantlet stages. Total proteins were extracted followed by tryptic enzyme digestion. The tryptic digested peptides were examined by nano LC-MS/ MS. Identified proteins were classified based on biological process, molecular function, and cellular components. Twenty-seven differentially expressed proteins were validated at the transcript level using qRT-PCR. These proteins were involved in plant growth and development, gene regulation, signalling, hormone response, and stress response. Moreover, the differentially expressed proteins were categorised and reported as the candidate proteins for the development of biomarkers, which could be used to differentiate the embryo’s developmental stages. The information on identified proteins obtained from this study will serve as the foundation for the understanding of the oil palm somatic embryogenesis in the tissue culture process.