Protein synthesis in plant crops contributes to the balance of food and fuel on our planet that influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to changing environmental cues via deposition of chemical modifications into rRNA. Here, we present the structure of a plant ribosome from tomato and quantitative mass spectrometry analysis of its rRNAs. The study reveals fine features of the ribosomal proteins, 71 plant-specific rRNA modifications, and re-annotates 30 rRNA residues in the available sequence. On the protein level, isoAsp is found in position 137 of uS11, and previously believed to be universal zinc finger is missing in eL34, suggesting a lower effect of zinc deficiency on protein synthesis in plants. On the rRNA level, the plant ribosome differs markedly from its human counterpart with respect to the spatial distribution of modifications. Thus, it represents an additional layer of gene expression regulation highlighting the molecular signature of a plant ribosome. The results provide a reference model of a plant ribosome for structural studies and an accurate marker for molecular ecology.