Summary High concentrations of sulfur dioxide (SO2) as an air pollutant, and its derivative sulfite, cause abiotic stress that can lead to cell death. It is currently unknown to what extent plant fumigation triggers specific transcriptional responses. To address this question, and to test the hypothesis that sulfite oxidase (SO) is acting in SO2 detoxification, we compared Arabidopsis wildtype (WT) and SO knockout lines (SO‐KO) facing the impact of 600 nl l−1 SO2, using RNAseq to quantify absolute transcript abundances. These transcriptome data were correlated to sulfur metabolism‐related enzyme activities and metabolites obtained from identical samples in a previous study. SO‐KO plants exhibited remarkable and broad regulative responses at the mRNA level, especially in transcripts related to sulfur metabolism enzymes, but also in those related to stress response and senescence. Focusing on SO regulation, no alterations were detectable in the WT, whereas in SO‐KO plants we found up‐regulation of two splice variants of the SO gene, although this gene is not functional in this line. Our data provide evidence for the highly specific coregulation between SO and sulfur‐related enzymes like APS reductase, and suggest two novel candidates for involvement in SO2 detoxification: an apoplastic peroxidase, and defensins as putative cysteine mass storages.