Carbonate-rich soils limit plant performance and crop production. Previously, local adaptation to carbonated soils was detected in wild Arabidopsis thaliana accessions, allowing the selection of two demes with contrasting phenotypes: A1 (carbonate tolerant, c+) and T6 (carbonate sensitive, c-). Here, A1 _(c+) and T6 _(c-) seedlings were grown hydroponically under control (pH 5.9) and bicarbonate conditions (10 mM NaHCO ₃, pH 8.3) to obtain ionomic profiles and conduct transcriptomic analysis. In parallel, A1 _(c+) and T6 _(c-) parental lines and their progeny were cultivated on carbonated soil to evaluate fitness and segregation patterns. To understand the genetic architecture beyond the contrasted phenotypes a bulk segregant analysis sequencing (BSA-Seq) was performed. Transcriptomics revealed 208 root and 2503 leaf differentially expressed genes (DEGs) in A1 _(c+) vs T6 _(c-) comparison under bicarbonate stress, mainly involved in iron, nitrogen and carbon metabolism, hormones, and glycosylates biosynthesis. Based on A1 _(c+) and T6 _(c-) genome contrasts and BSA-Seq analysis, 69 genes were associated with carbonate tolerance. Comparative analysis of genomics and transcriptomics discovered a final set of 18 genes involved in bicarbonate stress responses that may have relevant roles in soil carbonate tolerance.