The tricarboxylic acid citric acid is a key intermediary metabolite in organisms from all domains of the tree of life. Surprisingly, this metabolite specifically interacts with the light-induced signaling state of the photoactive yellow protein (PYP), such that, at 30 mM, it retards recovery of this state to the stable ground state of the protein with up to 30%, in the range from pH 4.5 to pH 7. We have performed a detailed UV/vis spectroscopic study of the recovery of the signaling state of wild type (WT) PYP and two mutants, H108F and Delta 25-PYP, derived from this protein, as a function of pH and the concentration of citric acid. This revealed that it is the dianionic form of citric acid that binds to the pB state of PYP. Its binding site is located in between the N-terminal cap and central beta-sheet of PYP, which is accessible only in the signaling state of the protein. The obtained results show how changes in the distribution of subspecies of the signaling state of PYP influence the rate of ground state recovery.