In bacterial reaction centers (RCs), changes of protonation state of carboxylic groups, of quinone-protein interactions as well as backbone rearrangements occuring upon QB photoreduction can be revealed by FTIR difference spectroscopy. The influence of compensatory mutations to the detrimental Asp L213 → Asn replacement on QB−/QB FTIR spectra of Rb. sphaeroides RCs was studied in three double mutants carrying a Asn M44 → Asp, Arg M233 → Cys, or Arg H177 → His suppressor mutation. The proton uptake by Glu L212 upon QB− formation, as reflected by the positive band at 1728 cm−1, is increased in the Asn M44 → Asp and Arg H177 → His suppressor RCs with respect to native RCs, and remains comparable to that observed in Asp L213 → Asn mutant RCs. Only the Arg M233 → Cys suppressor mutation affected the 1728 cm−1 band, reducing its amplitude to near native level. Thus, there is no clear correlation between the apparent extent of proton uptake by Glu L212 and the recovery of the proton transfer RC function. In all of the mutant spectra, several protein (amide I and amide II) and quinone anion (C...O/C...C) modes are perturbed compared to the spectrum of native RCs. These IR data show that all of the compensatory mutations alter the semiquinone-protein interactions and the backbone providing direct evidence of structural changes accompanying the restoration of efficient proton transfer in RCs containing the Asp L213 → Asn lesion.