A photo-chemically activated micro-bubble based root canal disinfection method for disinfecting a shaped root canal comprises (a) introducing a photoactive solution into the root canal, the photoactive solution containing a photoactive compound (such as methylene blue) dissolved in an alcohol carrier solution (such as polyethylene glycol and/or ethanol); (b) removing excess photoactive solution from the root canal; (c) introducing a micro-bubble solution comprised of an oxygen carrier (such as perfluorocarbon), an oxidizing agent (such as hydrogen peroxide) and a surfactant (such as a nonionic polyoxyethylene surfactant); (d) sonically or ultrasonically activating the micro-bubble solution in the canal; and (e) introducing light into the canal.