This is the second part of a comprehensive review article about photo-Fenton reaction at near-neutral pH used for water and wastewater disinfection. In this part, a critical revision of the fundamental physical, chemical and biological parameters affecting the photo-catalytic process efficiency are discussed. The effects of the chemical aspects, considered either as facilitators or competitors of photo-Fenton are deeply analyzed, with special focus on organic matter and its effect over bacterial inactivation. The role of solubilized iron and the biological nature of different pathogens are deeply assessed according to reported experimental data. Water temperature, turbidity, and radiation parameters like solar UV energy, ligh scattering and absorption during photo-Fenton are pictured in terms of treatment efficiency and suitable reactor design. Recent unconventional photo-Fenton strategies using iron chelates, iron oxides (including zero valent iron) and iron-based materials are also highlighted as new approaches to this process. Finally, the existing pilot scale studies in real conditions using photo-Fenton at near-neutral pH are revised, while alternative options and further research for real implementation are proposed. (C) 2016 Elsevier B.V. All rights reserved.