Protein-metabolite interactions (PMIs) are critical regulators of cellular processes, yet their roles in plant-pathogen interactions remain poorly understood. Here, we applied PROMIS (Protein-Metabolite Interactions using Size separation) to map the Arabidopsis protein-metabolite interactome during infection with Pseudomonas syringae pv. tomato DC3000 (Pto DC3000). PROMIS resolved elution profiles for >5,700 proteins and 192 annotated metabolites across infected, systemic, and control tissues, revealing infection-associated remodeling of protein assemblies and metabolite co-fractionation patterns. Integrating co-fractionation with coronatine-induced transcriptional responses, we identified NATA1, a polyamine N-acetyltransferase, as a coronatine-associated host protein binder. Biochemical assays confirmed direct coronatine-NATA1 interaction (Kd = 586 nM), whereas the homolog NATA2 did not bind coronatine. Coronatine did not strongly inhibit NATA1 catalytic turnover under our assay conditions but consistently depressed NATA1 dimer formation in vitro and in planta. In silico docking together with targeted mutational analyses identified a coronatine-sensitive interface on NATA1, revealing residue-specific coupling between ligand binding, assembly state, and acetyl-CoA engagement. Collectively, these findings establish PROMIS as a robust platform for infection-state PMI discovery and uncover a coronatine-responsive regulatory node that links small-molecule signaling to host polyamine acetylation.