Bacillus subtilis is able to use γ‐aminobutyric acid (GABA) found in the soil as carbon and nitrogen source, through the action of GABA aminotransferase (GabT) and succinic semialdehyde dehydrogenase (GabD). GABA acts as molecular effector in the transcriptional activation of the gabTD operon by GabR. GabR is the most studied member of the MocR family of prokaryotic pyridoxal 5′‐phosphate (PLP)‐dependent transcriptional regulators, yet crucial aspects of its mechanism of action are unknown. GabR binds to the gabTD promoter, but transcription is activated only when GABA is present. Here, we demonstrated, in contrast with what had been previously proposed, that three repeated nucleotide sequences in the promoter region, two direct repeats and one inverted repeat, are specifically recognized by GabR. We carried out in vitro and in vivo experiments using mutant forms of the gabTD promoter. Our results showed that GABA activates transcription by changing the modality of interaction between GabR and the recognized sequence repeats. A hypothetical model is proposed in which GabR exists in two alternative conformations that, respectively, prevent or promote transcription. According to this model, in the absence of GABA, GabR binds to DNA interacting with all three sequence repeats, overlapping the RNA polymerase binding site and therefore preventing transcription activation. On the other hand, when GABA binds to GabR, a conformational change of the protein leads to the release of the interaction with the inverted repeat, allowing transcription initiation by RNA polymerase. Bacillus subtilis uses ‐aminobutyrate (GABA) found in the soil as nitrogen source, through GABA aminotransferase (GabT) and succinic semialdehyde dehydrogenase (GabD). Transcription of the gabTD operon is activated by the transcriptional factor GabR upon binding of GABA. Our investigation demonstrates that, depending on whether GABA is absent or present, GabR differently interacts with two direct and one inverted repeats in the gabTDpromoter, respectively, preventing or promoting transcription activation.