Limiting the synthesis and activity of ribosomes is crucial for responding to various stresses, including nutrient starvation or proteotoxic stress. In Bacillus subtilis, this can be achieved through the coordinated action of the alarmones (p)ppGpp and the transcription factor Spx. In this study, we performed a genetic screen to identify new factors involved in the heat shock response of B. subtilis . We discovered that the RNase Y specificity factor Y-complex plays an important role in the heat shock response and the transition to the stationary growth phase. The Y-complex is required for the processing of various RNAs, including the maturation of mRNAs encoding proteins involved in translation and metabolism. We further demonstrate that the Y-complex and RNase Y initiate the degradation of rRNAs in mature ribosomes, lowering their abundance. We propose the Y-complex as a system by which B. subtilis regulates protein synthesis and resource allocation after exponential growth. ### Competing Interest Statement The authors have declared no competing interest. Max Planck Society Deutsche Forschungsgemeinschaft, https://ror.org/018mejw64