Plants are foundational for global ecological and economic systems, but most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. By using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified previously unknown interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical for agriculture. We also observed plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers a cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes. Display omitted •A global snapshot of protein organization in plants from deep proteomics profiling•Biochemical fractionation reveals stable protein complexes conserved across plants•Many observed complexes have previously only been inferred in plants by gene content•Known molecular modules are elaborated in plants with novel subunits and organization This massive plant proteomics project, using co-fractionation mass spectrometry to measure the amounts and associations of over two million proteins from 13 diverse plant species, reveals stable protein complexes shared across plant cells and provides a framework for interpreting plant genetics and mutant phenotypes.