Alteration of metabolic processes is a common adaptive response of plants to various stress conditions and is likely to be under complex regulatory control. To understand the metabolic responses to rhizotoxic treatments in Arabidopsis thaliana, transcriptome profiles of major carbon and amino acid metabolic pathways were compared among aluminum (Al), copper (Cu) and cadmium (Cd) ion and NaCl treatments with a similar level of severity. All stress treatments induced genes encoding enzymes for synthesizing trehalose and polyamine, as well as tryptophan-synthesizing enzymes previously identified as critical for resistance to various stresses. Genes encoding enzymes critical for ascorbic acid and spermine synthesis had higher specificity to Cd and NaCl among the genes upregulated by each stress. Major isoforms of malic enzymes and glutamate decarboxylases were more specifically upregulated by the Al treatment than were other genes; these enzymes belong to cellular pH-regulating pathways, namely the biochemical pH stat pathway and the γ-amino butyric acid shunt. Characterization of the grouped genes with higher Cu specificity indicated that amino acid degradation and sugar starvation-like symptoms were enhanced by Cu treatment. Pathway analysis in the trehalose synthesis pathway accounted for the activation of the pathway and for the accumulation of trehalose by all stressors. These metabolic alterations might form part of the tolerance mechanisms of Arabidopsis roots against rhizotoxic ions.