ABSTRACT Polyamines have vital functions in organisms, including bacteria, plants, and animals, with key roles in growth, development, and stress responses. Spermine/spermidine N 1-acetyl transferases (SSATs) regulate polyamine abundance by catalysing their N -acetylation, thereby reducing the pool of polyamines and producing other bioactive components. The regulatory mechanisms controlling SSAT enzymes are incompletely understood. Here, we investigate the biological role and regulation of the two SSAT isoforms present in Arabidopsis thaliana , N -ACETYLTRANSFERASE ACTIVITY (NATA) 1 and 2. We show that NATA2 is a heat-stable isoform, induced in response to heat. Intriguingly, a nata2 knockout mutation proved beneficial for growth and pathogen defence under heat stress in Arabidopsis, aligning with the stress-mitigating effect of polyamines. In contrast, the double knockout of nata1 and nata2 was lethal, highlighting the essential role of basal SSAT activity. Our numerous crystal structures of both NATAs, supported by functional assays, revealed that stress-produced acidic metabolites can selectively inhibit polyamine acetylation by occupying the NATA substrate-binding pocket. This environment-responsive regulation mechanism may allow Arabidopsis to adjust the deleterious action of NATAs under stress conditions, without eliminating the enzyme. More generally, metabolite-ensemble inhibition may be a novel paradigm for non-genetic feedback regulation of plant enzymes.