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Summary Boron toxicity is a world‐wide problem for crops, yet we have a limited understanding of the genetic responses and adaptive mechanisms to this stress in plants.We employed a cross‐species comparison between boron stress‐sensitiveArabidopsis thalianaand its boron stress‐tolerant extremophyte relativeSchrenkiella parvula, and a multi‐omics approach integrating genomics, transcriptomics, metabolomics and ionomics to assess plant responses and adaptations to boron stress.Schrenkiella parvulamaintains lower concentrations of total boron and free boric acid than Arabidopsis when grown with excess boron.Schrenkiella parvulaexcludes excess boron more efficiently than Arabidopsis, which we propose is partly driven by SpBOR5, a boron transporter that we functionally characterize in this study. Both species use cell walls as a partial sink for excess boron. When accumulated in the cytoplasm, excess boron appears to interrupt RNA metabolism. The extremophyteS. parvulafacilitates critical cellular processes while maintaining the pool of ribose‐containing compounds that can bind with boric acid.TheS. parvulatranscriptome is pre‐adapted to boron toxicity. It exhibits substantial overlaps with the Arabidopsis boron‐stress responsive transcriptome. Cell wall sequestration and increases in global transcript levels under excess boron conditions emerge as key mechanisms for sustaining plant growth under boron toxicity.