The new capacity of X-ray free-electron laser (XFEL) facilities to produce multi-color Xray femtosecond pulses paves the way to explore ultrafast phenomena in matter induced by X-ray photons. In the present study, we exploit the site selectivity and the high temporal resolution of a two-color X-ray femtosecond pump-probe sequence to investigate the isomerization of formamide. The pump pulse excites a particular atomic site in the molecule, while the probe pulse captures changes in the chemical environment at a remote atomic site. The response of the system is found to strongly depends on the nature of the excited site, and the core excitation provides a selective control on chemical bond breaking. In particular, we show that the N1s → π * transition favors the isomerization reaction in formamide and demonstrate the possibility to observe in real time the hydrogen migration by measuring the time-dependent chemical shifts with the X-ray probe pulse. This work opens a unique perspective for X-rayinduced photochemistry at XFEL facilities.