Methods and related apparatus for real-time process monitoring during laser-based refractive index modification of an intraocular lens. During in situ laser treatment of the IOL to modify the refractive index of the IOL material, a signal from the IOL is measured to determine the processing effect of the refractive index modification, and based on the determination, to adjust the laser system parameters to achieve intended processing result. The signal measured from the IOL may be a fluorescent signal induced by the treatment laser, a fluorescent signal induced by an external illumination source, a temporary photodarkening effect, a color change, or a refractive index change directly measured by phase stabilized OCT.