We have studied the relationship between the initial glass composition and the structural changes associated with laser-induced refractive index modification in a series of Er-Yb doped and undoped zinc phosphate glasses. White light microscopy and waveguide experiments are used together with Raman and fluorescence spectroscopy to characterize the structural changes. The correlation between Raman peak shifts and fluorescence from phosphorus-oxygen hole center (POHC) defects indicates that fs-laser writing results in a depolymerization of the phosphate glass network. The results also show that the exact glass composition should be taken into account when fabricating waveguide devices in phosphate glasses, in order to both expand the fs-laser processing conditions and maximize favorable morphological changes for 3-D photonic devices. © 2011 Optical Society of America.