Femtosecond pump-probe experiments are performed on flavin biomolecules isolated in an ion trap. Mass spectra of the photoinduced fragments show that the fragmentation pathways can be modified using two-color two-photon excitation. In particular, when an infrared probe pulse (810nm) is added subsequent to the first excitation step (excitation of the S1 state of flavin mononucleotide at 405nm), branching ratios between lumichrome and lumiflavin production are inverted relative to the single excitation case.