Ultrafast isomerization reactions underpin many processes in (bio)chemical systems and molecular materials. Understanding the coupled evolution of atomic and molecular structure during isomerization is paramount for control and rational design in molecular science. Here we report transient X-ray absorption studies of the photo-induced linkage isomerization of a Ru-based photochromic molecule. X-ray spectra reveal the spin and valence charge of the Ru atom and provide experimental evidence that metal-centered excited states mediate isomerization. Complementary X-ray spectra of the functional ligand S atoms probe the nuclear structural rearrangements, highlighting the formation of two metal-centered states with different metal-ligand bonding. These results address an essential open question regarding the relative roles of transient charge-transfer and metal-centered states in mediating photoisomerization. Global temporal and spectral data analysis combined with time-dependent density functional theory reveals a complex mechanism for photoisomerization with atomic details of the transient molecular and electronic structure not accessible by other means. Show Partial Abstract