Unique translational regulation during early animal development indicates that a similar mechanism may exist in plants. However, high-throughput ‘-omics’ studies in the model flowering plant Arabidopsis thaliana have previously focused on RNA sequencing and the proteome has remained elusive. Now, Dianjing Guo and colleagues report a nanoproteomic analysis of Arabidopsis embryos from the two-cell stage to the heart stage. Using this approach, the authors identify 5386 proteins in total, with between 27 and 2154 ‘stage-exclusive proteins’ (SEPs) involved in processes such as chromatin organisation, lipid modification and chlorophyll metabolism. One such SEP, ZYGOTIC ARREST 1 (ZAR1), is abundant during early cleavage stages, but protein levels drop at the heart stage despite RNA levels remaining high. In addition, the researchers use these data to unpick the dynamic changes that occur during early embryogenesis, including heterogeneity in ribosomal proteins, cellular location and transcriptional regulators. To unpick the relationship between mRNA and protein in early embryogenesis, the authors also construct RNA libraries for the same stages and reveal high positive across-gene correlation between mRNA and protein. Overall, these data provide a valuable resource for investigating RNA-protein dynamics and regulation during early Arabidopsis development.