The complex regulatory network inBacillus, known as quorum sensing, offers many opportunities to modify bacterial gene expression and hence to control bioprocesses. One target regulated by this mechanism is the activity of the PsrfApromoter, which is engaged in the formation of lipopeptide surfactin. It was hypothesised that deletion ofrapC,rapFandrapH, encoding for prominent Rap-phosphatases known to affect PsrfAactivity, would enhance surfactin production. Therefore, these genes were deleted in asfp+derivative ofB. subtilis168 with subsequent evaluation of quantitative data. Up to the maximum product formation of the reference strainB. subtilisKM1016 after 16 h of cultivation, the titers of therapdeletion mutants did not exceed the reference. However, an increase in both product yield per biomassYP/Xand specific surfactin productivityqsurfactinwas observed, without any considerable effect on the ComX activity. By extending the cultivation time, a 2.7-fold increase in surfactin titer was observed after 24 h for strain CT10 (ΔrapC) and a 2.5-fold increase for CT11 (ΔrapF) compared to the reference strain KM1016. In addition,YP/Xwas again increased for strains CT10 and CT11, with values of 1.33 g/g and 1.13 g/g, respectively. Interestingly, the effect on surfactin titer in strain CT12 (ΔrapH) was not as distinct, although it achieved the highest promoter activity (PsrfA-lacZ). The data presented support the possibility of involving the quorum sensing system ofBacillusin bioprocess control as shown here on the example of lipopeptide production.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13568-023-01555-6.