The alternative sigma factor σB of Bacillus subtilis is responsible for the induction of the large general stress regulon comprising approximately 150–200 genes. YqgZ, a member of the σB regulon, resembles the global regulator Spx of the diamide stress regulon in B. subtilis. In this work we conducted a comprehensive transcriptome and proteome analysis of the B. subtilis wild-type 168 and its isogenic ΔsigB and ΔyqgZ mutants following exposure to 4% (v/v) ethanol stress, which led to the characterization of a ‘subregulon’ within the general stress response that is regulated by YqgZ. Activation and induction of σB are necessary but not sufficient for a full expression of all general stress genes. Expression of 53 genes was found to be positively regulated and the expression of 18 genes was negatively affected by YqgZ. The identification of the negatively regulated group represents a so far uncharacterized regulatory phenomenon observed in the ΔsigB mutant background that can now be attributed to the function of YqgZ. Due to the strict σB-dependent expression of YqgZ it was renamed to MgsR (modulator of the general stress response).